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At least 937 records · Page 52Linked to original sources
PubMed2006

Genetic diversity, population structure, and conservation of Sophora moorcroftiana (Fabaceae), a shrub endemic to the Tibetan Plateau.

Sophora moorcroftiana is a perennial leguminous low shrub endemic to the middle reaches of Yarlung Zangbo River in Tibet. It is an important species to fix sand dunes and to avoid the formation of shifting sands; therefore, its progressive over-exploitation may enhance land desertification. The levels and distribution of genetic variability of this species were evaluated from 10 natural populations at 24 loci encoding 13 enzymes, using allozyme analysis by starch gel electrophoresis. Data obtained revealed moderate levels of genetic variation within populations (Pp=27.5%, Ap=1.5, Hep=0.122) and a considerable divergence among populations (FST=0.199). Significant positive correlations (r2=0.49, p<0.05; r2=0.46, p<0.05) were found between elevation and both mean number of alleles per locus (A) and gene diversity (He) in the studied populations of S. moorcroftiana. Lower genetic diversity in lower elevation populations might be due to the negative effects of human pressures and habitat fragmentation, to adaptation to high altitudes as a consequence of a peripatric speciation process, or to directional gene flow along the river basin from the source populations located in the west at higher altitudes. The evaluation of the degree of threat has led to the inclusion of this species in the category of EN ("endangered"), and conservation strategies for this endemic species are discussed on the basis of these findings.

Alleles↗
PubMed2004

Bayesian models for the analysis of genetic structure when populations are correlated.

MOTIVATION: Population allele frequencies are correlated when populations have a shared history or when they exchange genes. Unfortunately, most models for allele frequency and inference about population structure ignore this correlation. Recent analytical results show that among populations, correlations can be very high, which could affect estimates of population genetic structure. In this study, we propose a mixture beta model to characterize the allele frequency distribution among populations. This formulation incorporates the correlation among populations as well as extending the model to data with different clusters of populations. RESULTS: Using simulated data, we show that in general, the mixture model provides a good approximation of the among-population allele frequency distribution and a good estimate of correlation among populations. Results from fitting the mixture model to a dataset of genotypes at 377 autosomal microsatellite loci from human populations indicate high correlation among populations, which may not be appropriate to neglect. Traditional measures of population structure tend to overestimate the amount of genetic differentiation when correlation is neglected. Inference is performed in a Bayesian framework. CONTACT: fur@ohsu.edu.

Bayes Theorem↗
PubMed2001

Genetic variation and population structure in Oryza malampuzhaensis Krish. et Chand. endemic to Western Ghats, South India.

Oryza malampuzhaensis Krish. et Chand. (2n = 4x = 48; Poaceae, Oryza) is endemic to Western Ghats, South India, and shows a highly localized distribution over a small geographical area in this region. This is the most poorly understood taxon in genus Oryza and is often misidentified as O. officinalis owing to their close morphology. We assessed the nature and distribution of genetic variation among 11 populations of O. malampuzhaensis using random amplified polymorphic DNA markers. The analysis revealed low genetic variation in O. malampuzhaensis. Cluster analysis of pairwise genetic distances of populations revealed three distinct clusters and the grouping of populations largely corresponded to their geographical proximity. Restricted gene flow and a geography-dependent differentiation were evident among populations. The altitude-influenced differences in ecological factors among the natural habitats of the populations seem to be the cause of the geography-dependent differentiation. Genetically isolated smaller populations and a narrow genetic base in O. malampuzhaensis point to its vulnerability to genetic drift and genetic depauperation. Thus O. malampuzhaensis appears to be under the threat of extinction and needs to be conserved by use of suitable methods. The present study also identified molecular markers diagnostic for O. malampuzhaensis.

Altitude↗
PubMed2001

Study of Theileria annulata population structure during bovine infection and following transmission to ticks.

Tams1 is the polymorphic immunodominant merozoite-piroplasm surface protein of Theileria annulata. Evidence for selection of divergent forms of Tams1 has been obtained recently. This study was performed to address whether selection takes place during persistent infection of the bovine host or during passage through the Hyalomma tick vector. Four calves were infected with a T. annulata isolate representing multiple parasite genotypes. The development of the parasite population was analysed by denaturing gradient gel electrophoresis (DGGE) using the Tams1 gene as a marker. In addition, the parasitaemia was measured by a semi-quantitative reverse line blot hybridization assay in order to correlate Tams1 variation to changes in parasitaemia. It was found that both parasitaemia and parasite population displayed limited variation during persistent infection. Ticks were allowed to acquire T. annulata during 2 periods of the bovine infection. Tams1 alleles detected in ticks fed during acute infection were identical to the population in the bovine host. However, ticks fed during the carrier status acquired parasites showing a single Tams1 isotype that represented, in several cases, a minor population in the bovine host at the time of infestation. Although only a limited number of ticks were studied, these preliminary data suggest that specific parasite genotypes may be selected during tick transmission from a carrier animal.

Animals↗
PubMed2005

Population structure and colonization history of the olive fly, Bactrocera oleae (Diptera, Tephritidae).

The olive fly, Bactrocera oleae, is the major pest of olives in most commercial olive-growing regions worldwide. The species is abundant in the Mediterranean basin and has been introduced recently into California and Mexico, creating problems for quarantine protection and international trade. Here, we use nuclear microsatellite markers and mitochondrial sequences to examine the history of olive fly range expansion and colonization. Sampled populations span the current distribution of the olive fly worldwide, including South and Central Africa, Pakistan, Mediterranean Europe and Middle East, California, and Mexico. The Pakistani populations appear to be genetically well differentiated from the remaining populations, though rooting the origins of the species is problematic. Genetic similarity and assignment tests cluster the remaining populations into two genetic groups--Africa and a group including the Mediterranean basin and the American region. That Africa, and not the Mediterranean, is the origin of flies infesting cultivated olive is supported by the significantly greater genetic diversity at microsatellite loci in Africa relative to the Mediterranean area. The results also indicate that the recent invasion of olive flies in the American region most likely originated from the Mediterranean area.

Animals↗
PubMed2001

Population structure and ecology of a tropical rare rhizomatous species of teosinte Zea diploperennis (Gramineae).

One of the objectives of the Sierra de Manantlán Biosphere Reserve (Jalisco, México) is the conservation in situ of the teosinte Zea diploperennis Iltis, Doebley, Guzman & Pazzi. Zea diploperennis is perennial, shade intolerant and its 1-3 m shoots are architecturally similar to maize. Clonal growth is of the phalanx type. Genets are iteroparous (modules semelparous). The demography of seven module and genet populations was studied in seven sites representing three stages of old-field succession. Seven permanent one-meter-square plots were randomly established in each site. All genets initially present and those that became established during our study were mapped and labeled according to year of establishment. The magnitude of demographic fluctuations was greater in module populations. Genet population dynamics followed a seasonal rhythm with a maximum population size obtained at the onset of the rainy season. A relation was documented between percent annual mortality of a cohort and its age: the younger the cohort, the greater the mortality. This was a statistically significant relationship, Y = [sin(-0.288x + 1.657)]2 (r = 0.92, p < 0.01), where is proportion annual mortality of genets and is the age of the cohort. The maximum rates of genet mortality occurred during the rainy season when population densities were greatest. As a consequence, we postulate that competition occurs principally during the rainy season. Linear relationships were observed between rate of population increase of genets versus old-field successional stage and soil type. Those areas with poor soil (Ultisol), degraded soil or soils with similar physical characteristics could be rehabilitated by introducing Z. diploperennis. Such rehabilitation would achieve two distinct objectives, promote propagation of this rare endemic and reclaim areas that are susceptible to erosion and further degradation.

Biodegradation, Environmental↗
PubMed2003

Steady-state analysis of structured population models.

Our systematic formulation of nonlinear population models is based on the notion of the environmental condition. The defining property of the environmental condition is that individuals are independent of one another (and hence equations are linear) when this condition is prescribed (in principle as an arbitrary function of time, but when focussing on steady states we shall restrict to constant functions). The steady-state problem has two components: (i). the environmental condition should be such that the existing populations do neither grow nor decline; (ii). a feedback consistency condition relating the environmental condition to the community/population size and composition should hold. In this paper we develop, justify and analyse basic formalism under the assumption that individuals can be born in only finitely many possible states and that the environmental condition is fully characterized by finitely many numbers. The theory is illustrated by many examples. In addition to various simple toy models introduced for explanation purposes, these include a detailed elaboration of a cannibalism model and a general treatment of how genetic and physiological structure should be combined in a single model.

Cannibalism↗
PubMed2003

Population structure and variation in red snapper (Lutjanus campechanus) from the Gulf of Mexico and Atlantic coast of Florida as determined from mitochondrial DNA control region sequence.

The mitochondrial DNA control regions of red snapper (Lutjanus campechanus) from the Gulf of Mexico (n = 140) and Atlantic coast of Florida (n = 35) were sequenced to generate a prestocking genetic baseline for planned stock enhancement. Intrasample haplotype and nucleotide diversities ranged from 0.94 to 1.00 and 1.8% to 2.5%, respectively. All population analyses were consistent with the hypothesis that red snapper constitute a single, panmictic population over the sampled range. A ubiquitous, predominant haplotype, shared by 23% of the specimens, appeared to be evolutionarily recent, in contrast to previous findings based on restriction fragment length polymorphism data. Tajima's D values were suggestive of a recent bottleneck. Mismatch distributions from Gulf samples were smooth and unimodal, characteristic of recent population expansion. However, the Atlantic sample exhibited a comparatively broader, possibly multimodal distribution, suggestive of a more stable population history. Additional control-region data may clarify potentially disparate demographic histories of Gulf and Atlantic snapper.

Animals↗
PubMed2002

Evidence for population growth in humans is confounded by fine-scale population structure.

Although many studies have reported human polymorphism data, there has been no analysis of the effect of sampling design on the patterns of variability recovered. Here, we consider which factors affect a summary of the allele-frequency spectrum. The most important variable to emerge from our analysis is the number of ethnicities sampled: studies that sequence individuals from more ethnicities recover more rare alleles. These observations are consistent with fine-scale geographic differentiation as well as population growth. They suggest that the geographic sampling strategy should be considered carefully, especially when the aim is to infer the demographic history of humans.

Humans↗
PubMed2006

Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs).

Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms among 370 mostly sexually derived Citrus accessions from the collection of citrus germplasm maintained at the University of California, Riverside. A total of 275 alleles were detected with an average of 11.5 alleles per locus and an average polymorphism information content of 0.625. Genetic diversity statistics were calculated for each individual SSR marker, the entire population, and for specified Citrus groups. Phylogenetic relationships among all citrus accessions and putative non-hybrid Citrus accessions were determined by constructing neighbor-joining trees. There was strong support for monophyly at the species level when hybrid taxa were removed from the data set. Both of these trees indicate that Fortunella clusters within the genus Citrus but Poncirus is a sister genus to Citrus. Additionally, Citrus accessions were probabilistically assigned to populations or multiple populations if their genotype indicated an admixture by a model-based clustering approach. This approach identified five populations in this data set. These separate analyses (distance and model based) both support the hypothesis that there are only a few naturally occurring species of Citrus and most other types of Citrus arose through various hybridization events between these naturally occurring forms.

Alleles↗
PubMed1977

A demographic approach to population structure in Gyoda and Hasuda, Japan.

The mean inbreeding coefficients for Gyoda and Hasuda cities were 0.00295 for 600 couples and 0.00320 for 621 couples, respectively. The mean inbreeding coefficient decreased and the mean marital distance increased with a more recent year of marriage. The mean distances and its standard deviations between birthplaces of mates, father-offspring, mother-offspring, and sibs are 53.95 +/- 159.30 km, 43.38 +/- 174.29 km, 37.61 +/- 131.32 km and 9.42 +/- 66.39 km, respectively for the Gyoda population. These values are 98.49 +/- 270.77 km, 87.60 +/- 249.91 km, 60.05 +/- 193.63 km, and 16.36 +/- 64.64 km, respectively for the Hasuda population. The dimensionality of migration seems to be one.

Consanguinity↗
PubMed1990

Population structure of the human pseudoautosomal boundary.

The mammalian sex chromosomes are composed of two genetically distinct segments: the pseudoautosomal region, where recombination occurs between the X and Y chromosomes, and the sex chromosome-specific parts. Between these two segments the human sex chromosomes differ by the insertion of an Alu element on the Y chromosome. We have surveyed the sequence variation in the boundary region using the polymerase chain reaction. Fifty seven Y and sixty X chromosomes from ten different human populations were analysed. The X chromosomes were found to be polymorphic at five positions in a 300-base-pair region. By contrast, all Y chromosomes were identical except for one distal polymorphism shared with the X chromosome.

Base Sequence↗
PubMed1996

Clinical isolates of Histoplasma capsulatum from Indianapolis, Indiana, have a recombining population structure.

A sample of 30 clinical isolates of Histoplasma capsulatum was analyzed to determine (i) whether genetic exchange is important in the life cycle of this fungus and (ii) whether distinct subpopulations which correlate with disease severity or host immune status exist. Eleven biallelic molecular markers were developed, with the frequency of the least common allele at each molecular locus ranging from 10 to 50%. Every isolate had a different, unique multilocus genotype. Data analysis indicated that frequent recombination occurs within the Indianapolis, Ind., population. There were no associations between isolates from the immunocompromised population or from those with different clinical manifestations of histoplasmosis.

Genes, Fungal↗
PubMed2004

Population structure of a colony of dog guides.

The objective of this study was to describe changes in genetic diversity in a colony of dog guides since its founding. Two breeds, German Shepherds (GS) and Labrador Retrievers (LR), were evaluated. Data were pedigrees of 4,699 GS and 3,573 LR dogs bred for use as guides by The Seeing Eye, Inc., Morristown, NJ. Rapid increases in average pairwise numerator relationships occurred in both breeds, although the average was approximately one-third higher in the GS population than in the LR population. A similar trend was observed for average inbreeding. The rate of increase in inbreeding has slowed in recent generations. In the current generation, relationship and inbreeding for all animals averaged 25.3 and 26.2% in GS, and 15.5 and 22.0% in LR, respectively. Effective founder numbers initially decreased in GS until Generation 3, and then increased steadily. Effective founder number in LR constantly increased. There was a constant increase in effective founder number in LR. A similar pattern was noted for effective ancestor number as well. Founder genome equivalents were initially higher in GS but decreased over time in both breeds. Generation intervals averaged 23.7 mo in GS and 23.2 mo in LR. Sires had average service lives of 2.7 and 2.2 generations in GS and LR, respectively. Dams had average service lives of 2.1 generations in both breeds. Litter sizes averaged 5.1 and 7.4 pups per litter for GS and LR, respectively. Effective founder and ancestor numbers have slowly increased over time, and heterozygosity as measured by the number of founder genome equivalents in the population has increased. Limitations on the number of matings permitted for sires and service life of dams has led to a plateau for inbreeding and relationships. The importation of germplasm from other working dog colonies is desirable.

Animals↗
PubMed1997

Population structure in the spider mite Tetranychus urticae (Acari: Tetranychidae) from Crete based on multiple allozymes.

The polymorphism of four isozymes was studied on single females of Tetranychus urticae from Crete (Greece), using an isoelectric focusing technique. Genetic differentiation was found to be correlated with distance but not with the species of colonized host-plants. Thus no differentiation was observed between samples collected on citrus trees, tomato, pumpkin, okra or weed plants located within a 50 m(2) area, showing that at this geographical scale T. urticae populations are panmictic. In contrast, samples from plants at 150 m or more from one another displayed a significant genetic differentiation. These results are discussed in relation to the known pattern of migration in the species.

Journal Article↗
PubMed2006

Population structure, persistence, and seasonality of autochthonous Escherichia coli in temperate, coastal forest soil from a Great Lakes watershed.

The common occurrence of Escherichia coli in temperate soils has previously been reported, however, there are few studies to date to characterize its source, distribution, persistent capability and genetic diversity. In this study, undisturbed, forest soils within six randomly selected 0.5 m2 exclosure plots (covered by netting of 2.3 mm2 mesh size) were monitored from March to October 2003 for E. coli in order to describe its numerical and population characteristics. Culturable E. coli occurred in 88% of the samples collected, with overall mean counts of 16 MPN g(-1), ranging from < 1 to 1657 (n = 66). Escherichia coli counts did not correlate with substrate moisture content, air, or soil temperatures, suggesting that seasonality were not a strong factor in population density control. Mean E. coli counts in soil samples (n = 60) were significantly higher inside than immediately outside the exclosures; E. coli distribution within the exclosures was patchy. Repetitive extragenic palindromic polymerase chain reaction (Rep-PCR) demonstrated genetic heterogeneity of E. coli within and among exclosure sites, and the soil strains were genetically distinct from animal (E. coli) strains tested (i.e. gulls, terns, deer and most geese). These results suggest that E. coli can occur and persist for extended periods in undisturbed temperate forest soils independent of recent allochthonous input and season, and that the soil E. coli populations formed a cohesive phylogenetic group in comparison to the set of fecal strains with which they were compared. Thus, in assessing E. coli sources within a stream, it is important to differentiate background soil loadings from inputs derived from animal and human fecal contamination.

Animals↗
PubMed1994

Population structure of the Chenchu and other south Indian tribal groups: relationships between genetic, anthropometric, dermatoglyphic, geographic, and linguistic distances.

We describe the genetic structure and interrelationships of nine south Indian tribal groups (seven from Andhra Pradesh and two from the adjoining states of Tamil Nadu and Kerala) using seven polymorphic loci (ABO, MN, RH, PGM, ACP, PGD, and LDH). R matrix analysis indicates that the Andhra Pradesh tribes are clustered and that the Kadar and Irula are genetically isolated from them. This dispersion of populations has been explained by the combination of relatively high frequencies of the alleles RH D and MN M in the Kadar and the relatively high proportions of the allele PGM*2 in the Irula. The Mahaboobnagar Chenchu subgroup is isolated from other Telugu-speaking groups because of high frequencies of the PGM*1 and ACP*A alleles. The regression of mean per locus heterozygosity (H) on distance from the gene frequency centroid (rii) reveals considerable levels of external gene flow among the Lambadi, the Yerukula, and the two Chenchu subgroups and more homogeneity in the Kolam, Koya, Yanadi, Irula, and Kadar. Mantel statistics were used to assess the relative effects of nonbiological processes (i.e., language and geography) on the morphological and genetic patterns of these subdivided populations. The significance of correlations was determined between different data sets (genetic, dermatoglyphic, anthropometric, geographic, and linguistic) at three levels involving nine, six, and five populations. Although multiple correlation analysis reveals significant combined effects of geography and language on genetics, anthropometrics, and dermatoglyphics, highly significant partial correlations suggest strong effects of geography on both anthropometry and genetics. Our analysis indicates that geographic factors have an overwhelming effect on the genetic differentiation of the south Indian tribal groups.

Alleles↗
PubMed2004

Population structure and history of a phenotypically variable teiid lizard (Ameiva chrysolaema) from Hispaniola: the influence of a geologically complex island.

Ameiva chrysolaema is distributed across the island of Hispaniola in the West Indies. The species is restricted to dry lowlands between major mountain ranges and along the southern and eastern coasts. Phylogenetic and phylogeographic analyses of mtDNA sequence variation from 14 sampling localities identify at least three independent evolutionary lineages, separated from one another by major mountain ranges. Nested clade phylogeographic analysis (NCPA) suggests a complex history of population fragmentation, consistent with geological evidence of seawater incursions into the Azua and Enriquillo basins during the Pliocene/Pleistocene (approximately 1.6 mya). Significantly negative Fu's F(S) values and parameters of mismatch distributions suggest that formerly fragmented populations have recently expanded their ranges. Significantly large average population clade distances (APCD) for two sampling localities in the Azua basin suggest secondary contact at these localities of previously separated populations. The distribution of haplotypes among polymorphic populations of A. chrysolaema suggests that variation in dorsal pattern represents a polymorphism within evolutionary lineages. Ameiva leberi is ecologically indistinguishable from and syntopic with A. chrysolaema. Genetic data suggest that A. leberi is a junior synonym of A. chrysolaema.

Animals↗