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1.
Morihiro Notohara 《Journal of mathematical biology》1997,36(2):188-200
The distribution of the number of segregating sites among randomly sampled DNA sequences from a geographically structured
population is studied. We assume the infinitely-many-sites model of neutral genes and no recombination. Employing the genealogical
process, we derive an equation for the generating function of the distribution of the number of segregating sites. First we
study the strong-migration limit and prove that the distribution converges to that for a panmictic population. We also study
the case of two sampled DNA sequences in the d-dimensional torus model with homogeneous migration.
Received 13 July 1995; received in revised form 21 April 1997 相似文献
2.
Genetic variance, coefficient of parentage, and genetic distance of six soybean populations 总被引:4,自引:0,他引:4
T. Helms G. Vallad P. McClean J. Orf 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(1):20-26
Plant breeders would like to predict which biparental populations will have the largest genetic variance. If the population
genetic variance could be predicted using coefficient of parentage or genetic distance estimates based on molecular marker
data, breeders could choose parents that produced segregating populations with a large genetic variance. Three biparental
soybean {Glycine max (L.) Merr.} populations were developed by crossing parents that were closely related, based on pedigree relationships. Three
additional biparental populations were developed by crossing parents that were assumed to be unrelated. The genetic variance
of each population was estimated for yield, lodging, physiological maturity, and plant height. Coefficient of parentage was
calculated for each pair of parents used to develop the segregating populations. Genetic distance was determined, based on
the number of random amplified polymorphic markers (RAPD) that were polymorphic for each pair of parents. Genetic distance
was not associated with the coefficient of parentage or the magnitude of the genetic variance. The genetic variance pooled
across the three closely related populations was smaller than the genetic variance pooled across the three populations derived
from crossing unrelated parents for all four traits that were evaluated.
Received: 24 April 1996 / Accepted: 17 May 1996 相似文献
3.
Hilde M. Wilkinson-Herbots 《Journal of mathematical biology》1998,37(6):535-585
The structured coalescent is used to calculate some quantities relating to the genealogy of a pair of homologous genes and
to the degree of subpopulation differentiation, under a range of models of subdivided populations and assuming the infinite
alleles model of neutral mutation. The classical island and stepping-stone models of population structure are considered,
as well as two less symmetric models. For each model, we calculate the Laplace transform of the distribution of the coalescence
time of a pair of genes from specified locations and the corresponding mean and variance. These results are then used to calculate
the values of Wright’s coefficient F
ST
, its limit as the mutation rate tends to zero and the limit of its derivative with respect to the mutation rate as the mutation
rate tends to zero. From this derivative it is seen that F
ST
can depend strongly on the mutation rate, for example in the case of an essentially one-dimensional habitat with many subpopulations
where gene flow is restricted to neighbouring subpopulations.
Received: 1 October 1997 / Revised version: 15 March 1998 相似文献
4.
V. N. Zaitsev I. Zaitseva M. Papiz P. F. Lindley 《Journal of biological inorganic chemistry》1999,4(5):579-587
Ceruloplasmin is a multi-copper oxidase, which contains most of the copper present in the plasma. It is an acute-phase reactant that exhibits a two- to three-fold increase over the normal concentration of 300?μg/ml in adult plasma. However, the precise physiological role(s) of ceruloplasmin has been the subject of intensive debate and it is likely that the enzyme has a multi-functional role, including iron oxidase activity and the oxidation of biogenic amines. The three-dimensional X-ray structure of the human enzyme was elucidated in 1996 and showed that the molecule was composed of six cupredoxin-type domains arranged in a triangular array. There are six integral copper atoms per molecule (mononuclear sites in domains 2, 4 and 6 and a trinuclear site between domains 1 and 6) and two labile sites with roughly 50% occupancy. Further structural studies on the binding of metal cations by the enzyme indicated a putative mechanism for ferroxidase activity. In this paper we report medium-resolution X-ray studies (3.0–3.5?Å) which locate the binding sites for an inhibitor (azide) and various substrates [aromatic diamines, biogenic amines and (+)-lysergic acid diethylamide, LSD]. The binding site of the azide moiety is topologically equivalent to one of the sites reported for ascorbate oxidase. However, there are two distinct binding sites for amine substrates: aromatic diamines bind on the bottom of domain 4 remote from the mononuclear copper site, whereas the biogenic amine series typified by serotonin, epinephrine and dopa bind in close vicinity to that utilised by cations in domain 6 and close to the mononuclear copper. These binding sites are discussed in terms of possible oxidative mechanisms. The binding site for LSD is also reported. 相似文献
5.
We show that the number of segregating sites is a sufficient statistic for the scaled mutation parameter (θ) in the limit as the number of sites tends to infinity and there is free recombination between sites. We assume that the mutation parameter at each site tends to zero such than the total mutation parameter (θ) is constant in the limit. Our results show that Watterson’s estimator is the maximum likelihood estimator in this case, but that it estimates a composite parameter which is different for different mutation models. Some of our results hold when recombination is limited, because Watterson’s estimator is an unbiased, method-of-moments estimator regardless of the recombination rate. The quantity it estimates depends on the details of how mutations occur at each site. 相似文献
6.
The trace element contamination levels in mollusks were evaluated for different marine coastal sites in the Mediterranean
(Israeli coast), Red (Israeli coast) and North (German coast) Seas. Three bivalve species (Mactra corallina, Donax sp, and Mytilus
edulis) and two gastropod species (Patella sp.and Cellana rota) were sampled at polluted and relatively clean sites, and their soft tissue analyzed for Hg, Cd, Zn, Cu, Mn and Fe concentrations.
Representative samples were screened for organic contaminants [(DDE), polychlorinated biphenyls PCBs and polycyclic aromatic
hydrocarbons (PAHs)] which exhibited very low concentrations at all sites. In the Red Sea, the gastropod C. rota showed low levels of Hg (below detection limit) and similar Cd concentrations at all the examined sites, while other trace
elements (Cu, Zn, Mn, Fe) were slightly enriched at the northern beach stations. Along the Mediterranean coast of Israel,
Hg and Zn were enriched in two bivalves (M. corallina and Donax sp.) from Haifa Bay, both species undergoing a long-term decrease in Hg based on previous studies. Significant Cd and Zn enrichment
was detected in Patella sp. from the Kishon River estuary at the southern part of Haifa Bay. In general, Patella sp. and Donax sp. specimens from Haifa Bay exhibited higher levels of Cd compared to other sites along the Israeli Mediterranean coast,
attributed to the enrichment of Cd in suspended particulate matter. Along the German coast (North Sea) M. edulis exhibited higher concentrations of Hg and Cd at the Elbe and Eider estuaries, but with levels below those found in polluted
sites elsewhere.
Received: 25 February 1999 / Received in revised form: 22 April 1999 / Accepted: 30 April 1999 相似文献
7.
A. van Tuinen M. Koornneef M. -M. Cordonnier-Pratt L. H. Pratt R. Verkerk P. Zabel 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(1):115-122
The map positions of five previously described phytochrome genes have been determined in tomato (Lycopersicon esculentum Mill.) The position of the yg-2 gene on chromosome 12 has been confirmed and the classical map revised. The position of the phytochrome A (phy A)-deficient
fri mutants has been refined by revising the classical map of chromosome 10. The position of the PhyA gene is indistinguishable from that of the fri locus. The putative phyB1-deficient tri mutants were mapped by classical and RFLP analysis to chromosome 1. The PhyB1 gene, as predicted, was located at the same position. Several mutants with the high pigment (hp) phenotype, which exaggerates phytochrome responses, have been reported. Allelism tests confirmed that the hp-2 mutant is not allelic to other previously described hp (proposed here to be called hp-1) mutants and a second stronger hp-2 allele (hp-2
j
) was identified. The hp-2 gene was mapped to the classical, as well as the RFLP, map of chromosome 1.
Received: 24 May 1996 / Accepted: 14 June 1996 相似文献
8.
Summary. In eudicot postmeiotic tetrads, apertures are usually joined in pairs in highly conserved areas. These appear to be located
at the last points of contact persisting at the end of cytokinesis between the cytoplasm of the future microspores. In order
to investigate the relationship between cytokinesis and aperture formation, aperture distribution within postmeiotic tetrads
and the progression of meiosis were studied in Nicotiana tabacum cv. Ambalema. This variety (inbred line) produces about 85% tricolporate pollen and 15% tetracolporate pollen grains. In
addition, about 7% of tetrads are composed of four equal-sized microspores and a supernumerary pseudomicrospore of small size
and an equal proportion of tetrads exhibit unpaired apertures (these apertures are not joined in pairs within tetrads). Observation
of cytokinesis indicates that both unpaired apertures and pseudomicrospores could result from the persistence of late communications
between microsporocytes. Observations of tetrads indicate that an increase in the number of elements that are separated during
cytokinesis is correlated with an increase in microspore aperture number. All data converge to support the hypothesis that
aperture site determination is partly controlled by the number of walls formed to separate the different elements of the tetrad.
Received May 22, 2002; accepted October 29, 2002; published online April 2, 2003
RID="*"
ID="*" Correspondence and reprints: Laboratoire de Ecologie, Systematique et Evolution, Batiment 362, Université Paris Sud,
91405 Orsay cedex, France. 相似文献
9.
C. Taylor K. Madsen S. Borg M. C. Møller B. Boelt P. H. Holm 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,103(4):648-658
Genetic analysis, particularly the development of genetic linkage maps in forage grass species, lags well behind other members
of the Poaceae. Comparative mapping within this family has revealed extensive conservation in gene and marker synteny among chromosomes
of diverse genera. Recently, the ability to transfer mapped STS markers between barley and wheat has been demonstrated. The
transfer of mapped STS markers between cereals and forage grasses could provide PCR-based markers for comparative mapping
in these species providing they amplify homologous sequences. In this study, primers derived from three barley genes of defined
function and a gene from Phalaris coerulescens were used to amplify homologous fragments in Lolium perenne. Primers derived from two barley and two oat cDNA clones were also tested along with eight barley and two Triticum tauchii STS markers. Twenty one primer pairs derived from 18 loci were tested. Eleven primer pairs (52%) amplified homologous sequences
in L. perenne from ten (55%) of the loci targetted. Thirteen new STS markers were generated in L. perenne, of which ten have been mapped in barley or rye and amplify homologous sequences in L. perenne.
Received: 20 October 2000 / Accepted: 13 January 2001 相似文献
10.
Flow cytometric analysis of the chromosomes and stability of a wheat cell-culture line 总被引:3,自引:0,他引:3
T. Schwarzacher M. L. Wang A. R. Leitch G. Moore J. S. Heslop-Harrison N. Miller 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(1):91-97
A rapidly growing, long-term suspension culture derived from Triticum aestivum L. (wheat) was synchronized using hydroxyurea and colchicine, and a chromosome suspension with chromosomes was made. After staining with the DNA-specific fluorochromes Hoechst 33258 and Chromomycin univariate and bivariate flow-cytometry histograms showed 15 clearly resolved peaks corresponding to individual chromosome
types or groups of chromosomes with similar DNA contents. The flow karyotype was closely similar to a histogram of DNA content
measurements of Feulgen-stained chromosomes made by microdensitometry. We were able to show the stability of the flow karyotype
of the cell line over a year, while a parallel subculture had a slightly different, stable, karyotype following different
growth conditions. The data indicate that flow cytometric analysis of plant karyotypes enables accurate, statistically precise
chromosome classification and karyotyping of cereals. There was little overlap between individual flow-histogram peaks, so
the method is useful for flow sorting and the construction of chromosome specific-recombinant DNA libraries. Using bivariate
analysis, the AT:GC ratio of all the chromosomes was remarkably similar, in striking contrast to mammalian flow karyotypes.
We speculate about a fundamental difference in organization and homogenization of DNA sequences between chromosomes within
mammalian and plant genomes.
Received: 24 April 1996 / Accepted: 24 May 1996 相似文献
11.
Castor Muñoz Sobrino Pabio Ramil-Rego Manuel Antonio Rodríguez Guitián 《Vegetation History and Archaeobotany》2001,10(1):7-21
A new core taken from a site in the Sierra de Courel range of mountains in the northwest Iberian peninsula, Spain, enables
a palaeoenvironmental reconstruction to be made of the biological events resulting from climatic changes and human activities
during the last 17,000 years in the area. The sequence begins with a phase characterised by the dominance of Gramineae (Poaceae)
and Pinus. A markedly arid period with prevalence of Artemisia pollen occurred between 17,5000 and 15,500 uncal. B.P. Subsequently, a succession of woodlands with Betula, Pinus and other mesophilous and thermophilous trees was recognised during the period 15,500-13,500 uncal. B.P. Between 13,500 and
10,300 uncal. B.P. herbaceous vegetation formations indicating moister conditions dominated the pollen record, although a
maximum of Gramineae has been dated during the period 11,300-10,300 uncal. B.P. Comparison with other pollen data from neighbouring
mountains allows an interpretation of the vegetation changes during the glacial/interglacial transition in the mountains of
northwest Iberia. The Holocene pollen record from the site does not differ markedly from other records in the area, tree expansion
occurring before 10,000 uncal. B.P. and high values of deciduous Quercus mixed with other trees and shrubs persisting until 3500 uncal. B.P., when increased human activities are shown by a fall
of the tree pollen percentages.
Received July 7, 1999 / Accepted May 22, 2000 相似文献
12.
The phenological calendar of Estonia and its correlation with mean air temperature 总被引:13,自引:0,他引:13
A phenological calendar with 24 phenological phases was compiled for three meteorological stations in Estonia for the period
1948–1996. We analysed the length of the vegetation period, the order of the phenological phases, and the variability and
possible changes for two incremental climate change scenarios (±2°C), and compared the results with examples of extreme years.
The statistically significant linear trends show that the spring and summer-time phenological phases occurred earlier and
the autumn phases moved later during the study period. The study of extreme (minimum and maximum) years shows that 70% of
the earliest dates of the 24 phases studied have occurred during the last 15 years with an absolute maximum in 1990 with 8
extreme phases. The phenological spring has shortened (slope –0.23), the summer period has lengthened (slope 0.04), and the
autumn has lengthened too. The length of the growing season, determined by the vegetation of rye, has shortened (slope –0.09),
which could be the result of changing agricultural technology. The correlation between the starting dates of the phenological
phases with the air temperature of the previous 2–3 months is relatively high (0.6–0.8). Studying the +2°C and –2°C scenarios
and values for the extreme years shows that, in the case of short variations of air temperature, the phenological development
remains within the limits of natural variation.
Received: 29 November 1999 / Revised: 15 May 2000 / Accepted: 16 May 2000 相似文献
13.
In an unpredictable environment, the distributions of alleles from which polymorphism can be maintained forever belong to
a certain set, the C-viability kernel. Such a set is calculated in the two-locus haploid model, as well as the corresponding fitnesses at any time which make this
maintenance possible. The dependence of the C-viability kernel on the set U of admissible fitnesses and on the recombination rate r is studied. Notably, the C-viability kernel varies rapidly in the neighborhood of equal fitness of AB and ab; it becomes empty when ab has a fitness below a certain function, which is delineated, of the recombination rate. The properties of the two-locus model
under constraints, out of equilibrium and with unpredictable selection are thus presented.
Received: 20 May 1999 相似文献
14.
Megumi Ehara Yasuko Hayashi-Ishimaru Yuji Inagaki Takeshi Ohama 《Journal of molecular evolution》1997,45(2):119-124
Several algae that were previously classified in the phylum Xanthophyta (yellow-green algae) were assigned in 1971 to a new
phylum, Eustigmatophyta. It was anticipated that the number of algae reclassified to Eustigmatophyta would increase. However,
due to the fact that the morphological characteristics that segregate eustigmatophytes from other closely related algae can
be only obtained through laborious electron microscopic techniques, the number of members in this phylum have increased rather
slowly. We attempted, therefore, to segregate two closely related groups of algae, eustigmatophytes and yellow-green algae,
on the basis of a molecular phylogenetic tree as a means of providing an alternative method of distinguishing these phyla.
We analyzed the mitochondrial cytochrome oxidase subunit I (COXI) gene sequences of eight algae classified as xanthophyceans and found that six manifested the expected deviant genetic code
where AUA codes for methionine (AUA/Met), but not for isoleucine (AUA/Ile) as in the universal genetic code. The other two,
Monodus sp. (CCMP 505) and Ophiocytium majus (CCAP 855/1), which were presumed to be yellow-green algae, and all the examined eustigmatophytes utilized AUA for Ile. In
addition, the phylogenetic tree of COXI gene sequences showed that the six yellow-green algae bearing the AUA/Met deviant code composed a tight clade with a bootstrap
value of 100%. The phylogenetic tree of the corresponding sequences from Monodus sp. and Ophiocytium majus and the eustigmatophytes also composed a tight cluster, but with a bootstrap value of 92%. These results strongly suggest
that two previously classified members of yellow-green algae belong to the phylum Eustigmatophyta. Therefore, examination
of the mitochondrial genetic code in algae appears to be a potentially very useful genetic marker for classifying these organisms,
especially when it is considered with the results obtained through a molecular phylogenetic tree.
Received: 14 December 1996 / Accepted: 3 April 1997 相似文献
15.
M. P. Koshy G. Namkoong J. H. Roberds 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,97(5-6):990-993
Either by selective breeding for population divergence or by using natural population differences, F2 and advanced generation hybrids can be developed with high variances. We relate the size of the genetic variance to the population
divergence based on a forward and backward mutation model at a locus with two alleles with additive gene action. The effects
of population size and initial gene frequency are also explored. Larger parental population sizes increase the F2 genetic variance if the initial probability distribution is uniform or U-shaped. However, population size has the opposite
effect if the initial distribution of gene frequencies is skewed such as it would be with newly arriving alleles. These alleles
contribute to the genetic variance sooner when the selection pressure is higher or when the effective population size is smaller.
Received: 5 April 1998 / Accepted: 22 April 1998 相似文献
16.
The rate of expansion of bacterial colonies of S. liquefaciens is investigated in terms of a mathematical model that combines biological as well as hydrodynamic processes. The relative
importance of cell differentiation and production of an extracellular wetting agent to bacterial swarming is explored using
a continuum representation. The model incorporates aspects of thin film flow with variable suspension viscosity, wetting,
and cell differentiation. Experimental evidence suggests that the bacterial colony is highly sensitive to its environment
and that a variety of mechanisms are exploited in order to proliferate on a variety of surfaces. It is found that a combination
of effects are required to reproduce the variation of bacterial colony motility over a large range of nutrient availability
and medium hardness.
Received: 29 April 1999 相似文献
17.
18.
The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to be polymorphic. This distribution is widely used in population genetic inferences, including statistical tests of neutrality in which a skew in the observed frequency spectrum across independent sites is taken as a signature of departure from neutral evolution. Theoretical aspects of the frequency spectrum have been well studied and several interesting results are available, but they are usually under the assumption that a site has undergone at most one mutation event in the history of the sample. Here, we extend previous theoretical results by allowing for at most two mutation events per site, under a general finite allele model in which the mutation rate is independent of current allelic state but the transition matrix is otherwise completely arbitrary. Our results apply to both nested and nonnested mutations. Only the former has been addressed previously, whereas here we show it is the latter that is more likely to be observed except for very small sample sizes. Further, for any mutation transition matrix, we obtain the joint sample frequency spectrum of the two mutant alleles at a triallelic site, and derive a closed-form formula for the expected age of the younger of the two mutations given their frequencies in the population. Several large-scale resequencing projects for various species are presently under way and the resulting data will include some triallelic polymorphisms. The theoretical results described in this paper should prove useful in population genomic analyses of such data. 相似文献
19.
T. Krugman A. Korol E. Nevo J. W. Snape O. Levy B. Rubin 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(1):46-51
Chlorotoluron is a selective phenylurea herbicide widely used for broad-leaved and annual grass weed control in cereals. Variation in the response to chlorotoluron (CT) was found in both hexaploid bread wheat (Triticum aestivum L.) and wild tetraploid wheat (Triticum dicoccoides KöRN.). Here, we describe the comparative mapping of the CT resistance gene (Su1) on chromosome 6B in bread and wild wheat using RFLP markers. In bread wheat, mapping was based on 58 F4 single-seed descent (SSD) plants of the cross between a genotype sensitive to chlorotoluron, ‘Chinese Spring’ (CS), and a resistant derivative, the single chromosome substitution line, CS (‘Cappele-Desprez’ 6B) [CS (CAP6B). In T dicoccoides, mapping was based on 37 F2 plants obtained from the cross between the CT-susceptible accession B-7 and the resistant accession B-35. Nine RFLP probes spanning the centromere were chosen for mapping. In bread wheat Su1 was found to be linked to α-Amy-1 (9.84 cM) and Xpsr371 (5.2 cM), both on the long arm of 6B, and Nor2 (2.74 cM) on the short arm. In wild wheat the most probable linkage map was Nor2-Xpsr312-Su1-Pgk2, and the genetic distances between the genes were 24.8cM, 5.3cM, and 6.8cM, respectively. These results along with other published map data indicate that the linear order of the genes is similar to that found in T. aestivum. The results of this study also show that the Su1 gene for differential response to chlorotoluron has evolved prior to the domestication of cultivated wheat and not in response to the development and use of chemicals. 相似文献
20.
Mapping of the Rf-3 nuclear fertility-restoring gene for WA cytoplasmic male sterility in rice using RAPD and RFLP markers 总被引:24,自引:0,他引:24
G. Zhang Y. Lu T. S. Bharaj S. S. Virmani N. Huang 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(1):27-33
The cytoplasmic male sterility (CMS) of wild-abortive (WA) cytoplasm has been widely used for breeding hybrid rice. Two restorer
genes for the CMS have been found by traditional genetic analysis. To tag the restorer genes we used a set of near-isogenic
lines (NILs) of Zhenshan 97 carrying different genotypes for fertility restoration from IR24, to perform RAPD analysis. From
the survey of 720 random primers, six RAPD markers were identified to be associated with Rf-3. Three of these OPK05-800, OPU10-1100 and OPW01-350, were mapped on chromosome 1. Two populations from the crosses between Zhenshan 97 A and a near-isogenic restorer line ZSR21 and between Zhenshan 97 A and
IR24 were used for mapping Rf-3. The three RAPD markers and three RFLP markers, RG532, RG140 and RG458, were found to be closely linked to Rf-3 in the two populations. The same location of Rf-3 was also found in a population from the cross of IR58025 A//IR36/IR58025 B. At the RG532 locus, different alleles were found between two CMS
lines, Zhenshan 97 A and IR58025 A, and between two restorer lines, IR24 and IR36. The use of these molecular markers closely
linked to Rf-3 in facilitating the development of hybrid rice is discussed.
Received: 3 January 1996 / Accepted: 17 May 1996 相似文献