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1.
We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an approximation to the coalescent suggested by McVean and Cardin, and by Marjoram and Wall. Within this algorithm we compute, for two individuals randomly sampled from the population, the correlation between times to the most recent common ancestor and the linkage probability corresponding to two different loci with recombination rate R between them. These quantities characterise the linkage between the two loci in question. We find that the sequential Markov coalescent method approximates the coalescent well in general in models with demographic structure. An exception is the case where individuals are sampled from populations separated by reduced gene flow. In this situation, the correlations may be significantly underestimated. We explain why this is the case. 相似文献
2.
Odo Diekmann Mats Gyllenberg J. A. J. Metz Horst R. Thieme 《Journal of mathematical biology》1998,36(4):349-388
—We define a linear physiologically structured population model by two rules, one for reproduction and one for “movement”
and survival. We use these ingredients to give a constructive definition of next-population-state operators. For the autonomous
case we define the basic reproduction ratio R
0 and the Malthusian parameter r and we compute the resolvent in terms of the Laplace transform of the ingredients. A key feature of our approach is that
unbounded operators are avoided throughout. This will facilitate the treatment of nonlinear models as a next step.
Received 26 July 1996; received in revised form 3 September 1997 相似文献
3.
The effect of overcompensatory recruitment and the combined effect of overcompensatory recruitment and generation delay in
discrete nonlinear age-structured population models is studied. Considering overcompensatory recruitment alone, we present
formal proofs of the supercritical nature of bifurcations (both flip and Hopf) as well as an extensive analysis of dynamics
in unstable parameter regions. One important finding here is that in case of small and moderate year to year survival probabilities
there are large regions in parameter space where the qualitative behaviour found in a general n+1 dimensional model is retained already in a one-dimensional model. Another result is that the dynamics at or near the boundary
of parameter space may be very complicated. Generally, generation delay is found to act as a destabilizing effect but its
effect on dynamics is by no means unique. The most profound effect occurs in the n-generation delay cases. In these cases there is no stable equilibrium X
* at all, but whenever X
* small, a stable cycle of period n+1 where the periodic points in the cycle are on a very special form. In other cases generation delay does not alter the dynamics
in any substantial way.
Received 25 April 1995; received in revised form 21 November 1995 相似文献
4.
5.
Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic. However, most populations are structured. This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates. To develop a coalescent method unhampered by population structure, we perform two analyses. First, we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation(one generation back)is independent of population structure. Second, motivated by this finding, we propose a new coalescent method: i-coalescent analysis. The i-coalescent analysis computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles. Using simulated data, we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations, although we find this method often requires larger sample sizes for structured populations than for panmictic populations. Overall, our results indicate i-coalescent analysis to be a useful tool, especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms. 相似文献
6.
Schreiber SJ 《Journal of mathematical biology》2001,42(3):239-260
A class of truncated unimodal discrete-time single species models for which low or high densities result in extinction in
the following generation are considered. A classification of the dynamics of these maps into five types is proven: (i) extinction
in finite time for all initial densities, (ii) semistability in which all orbits tend toward the origin or a semi-stable fixed
point, (iii) bistability for which the origin and an interval bounded away from the origin are attracting, (iv) chaotic semistability
in which there is an interval of chaotic dynamics whose compliment lies in the origin’s basin of attraction and (v) essential
extinction in which almost every (but not every) initial population density leads to extinction in finite time. Applying these
results to the Logistic, Ricker and generalized Beverton-Holt maps with constant harvesting rates, two birfurcations are shown
to lead to sudden population disappearances: a saddle node bifurcation corresponding to a transition from bistability to extinction
and a chaotic blue sky catastrophe corresponding to a transition from bistability to essential extinction.
Received: 14 February 2000 / Revised version: 15 August 2000 / Published online: 16 February 2001 相似文献
7.
In this paper we propose a general framework for discrete time one-dimensional Markov population models which is based on
two fundamental premises in population dynamics. We show that this framework incorporates both earlier population models,
like the Ricker and Hassell models, and experimental observations concerning the structure of density dependence. The two
fundamental premises of population dynamics are sufficient to guarantee that the model will exhibit chaotic behaviour for
high values of the natural growth and the density-dependent feedback, and this observation is independent of the particular
structure of the model. We also study these models when the environment of the population varies stochastically and address
the question under what conditions we can find an invariant probability distribution for the population under consideration.
The sufficient conditions for this stochastic stability that we derive are of some interest, since studying certain statistical
characteristics of these stochastic population processes may only be possible if the process converges to such an invariant
distribution.
Received 15 May 1995; received in revised form 17 April 1996 相似文献
8.
Genetic variation and structure of ten wild, three domesticated and one wild-cultivated populations of pepper (Capsicum annuum) from northwestern Mexico were studied in order to find out if the domestication process has reduced the genetic variation
of the modern cultivars of this species. The analysis was based on 12 polymorphic loci from nine isozymes. Wild populations
were sampled in different habitats along a latitudinal gradient of ca. 500 km. All populations had high genetic variation
(i.e. wild: A = 2.72, P = 90.8%, He = 0.445; wild-cultivated: A = 2.50, P = 92.3%, He = 0.461; domesticated: A = 2.60, P = 84.6%, He = 0.408), indicating little genetic erosion in modern cultivars of pepper. Genetic diversity estimated by Nei's method showed
that most genetic variation is found within, rather than among populations. However, genetic differentiation is greater among
cultivated (G
ST=0.167) than among wild (G
ST=0.056) populations. Wild populations had an average genetic identity (I) of 0.952, indicating little differentiation and high gene flow (Nm=4.21) among these populations. Average genetic identity between wild and domesticated populations was of I=0.818, revealing that the domestication process has modified the genetic composition of commercial varieties of pepper. Changes
in genetic composition among commercial varieties seem to have occurred in different directions, as indicated by the average
value of I = 0.817 among these populations. The high level of diversity found in wild populations of C. annuum suggests that the wild relatives of cultivated peppers are a valuable genetic resource which must be conserved.
Received May 5, 1999 Accepted October 30, 2000 相似文献
9.
In this paper, a mathematical model is proposed to study the depletion of resources in a forest habitat due to the increase
of both population and pollution. It is shown that if the rate of pollutant emission into the environment is either population
dependent, constant, or periodic, the equilibrium biomass density of the resource settles down to a lower equilibrium than
its original carrying capacity, the magnitude of which decreases as the equilibrium levels of the density of population and
the concentration of pollutant increase. However, in the case of an instantaneous spill of pollutant into the environment,
the equilibrium biomass density decreases with the increase of the equilibrium density of population only. It is found that
if the population density and the emission rate of pollutant increase without control, the forestry resource may become extinct.
A conservation model is also proposed, the analysis of which shows that the resource biomass can be maintained at a desired
level by conserving the forestry resource and by controlling the growth of population and the emission rate of pollutant in
the habitat.
Received 1 June 1993; received in revised form 1 January 1997 相似文献
10.
Genetic diversity and structure in a natural Elymus caninus population from Denmark based on microsatellite and isozyme analyses 总被引:1,自引:0,他引:1
Genetic diversity in a natural Elymus caninus population from Denmark was assessed using isozyme and microsatellite markers. A total of 119 individuals from 46 maternal
plants were assayed. Microsatellite loci are shown to display higher levels of variation than isozyme loci. The mean number
of alleles per locus was 1.04 for isozymes and 1.38 for microsatellites. The percentage of polymorphic loci for isozymes and
microsatellites was 4.7% and 23.6% across the maternal plant, respectively. The genetic diversity at population level was
0.1 for isozymes, and 0.63 for microsatellites. The mean genetic diversity at maternal plant level was 0.027 for isozyme loci
and 0.117 for microsatellite loci. The average of total allozyme diversity (HT) was 0.22. The average of total microsatellite diversity was 0.56. Isozyme and microsatellite variation showed the same pattern
of differentiation between maternal plants. More than 75% total genetic diversity was found among maternal plants. About 25%
total genetic diversity was detected within maternal plants. Ten (22.7%) maternal plants produced heterozygous offspring at
allozyme loci, and 30 (68.2%) maternal plants gave heterozygous offspring at microsatellite loci. Both types of markers revealed
a relatively high genetic diversity in this population.
Received November 7, 2000 Accepted February 15, 2001 相似文献
11.
A. I. Granovitch 《Helgoland Marine Research》1999,53(1):9-18
The analysis of population systems is carried out on the basis of the spatial and functional classification of populations
developed by V.N. Beklemishev. The population system is a functional part of a particular community. Steady interrelationships
between population systems of different species within the community (referred to as ”community links”) appear to be a prerequisite
for the formation of a complex of population systems. A prominent example of this is the parasitic system. The parasitic system
is the population system of a parasite with all the connected populations of its hosts. The complexity of a parasitic system
depends on: (1) peculiarities of the life cycle of the parasite, since its population system is the organizing component of
the parasitic system and (2) subdivision of the environment for the parasites. The first trait is discussed from the standpoint
of the phase structure of populations, which is clearly seen in parasites. The second one comprises the organization of the
parasites’ environment according to the scale of variability (interspecies, interpopulation or intrapopulation) of hosts.
These make it possible to recognize spatial and functional parts in the framework of the parasitic system. A critical review
of the terminology is presented together with a list of the pertaining vocabulary.
Received: 15 January 1998 / Accepted: 15 October 1998 相似文献
12.
L.-z. Gao S. G. De-y. Hong 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(3):494-502
In order to determine the genetic diversity and genetic structure of populations in common wild rice Oryza rufipogon, an endangered species, allozyme diversity was analyzed using 22 loci in 607 individuals of 21 natural populations from the
Guangxi, Guangdong, Hainan, Yunnan, Hunan, Jiangxi and Fujian provinces in China. The populations studied showed a moderate
allozyme variability (A=1.33, P=22.7%, Ho=0.033 and He=0.068), which was relatively high for the genus Oryza. The levels of genetic diversity for Guangxi and Guangdong were significantly higher than those for the other regions, and
thus South China appeared to be the center of genetic diversity of O. rufipogon in China. A moderate genetic differentiation (FST=0.310, I=0.964) was found among the populations studied. Interestingly, the pattern of population differentiation does not
correspond to geographic distance. An estimate of the outcrossing rate (t=0.324) suggests that the species has a typical mixed-mating
system. The deficit of heterozygotes (F=0.511) indicates that some inbreeding may have taken place in outcrossing asexual
populations because of intra-clone outcrossing events and ”isolation by distance” as a result of human disturbance. In order
to predict the long-term genetic survival of fragmented populations, further studies on gene flow among the remaining populations
and the genetic effects of fragmentation are proposed. Finally, some implications for the conservation of endangered species
are suggested.
Received: 22 June 1999 / Accepted: 20 December 1999 相似文献
13.
Tight linkage may cause a reduction of nucleotide diversity in a chromosomal region if an advantageous mutation appears in
that region which is driven to fixation by directional selection. This process is usually called genetic hitchhiking. If selection
is strong, the entire process takes place during a time period of length 2s ln (2N) that is very short relative to 2N generations [s is the selection coefficient of the advantageous mutation and N the effective diploid population size]. On the time scale of 2N generations, which is characteristic for neutral evolution, we may therefore call this process a hitchhiking event. Using
coalescent methods, we analyzed a model in which a hitchhiking event occurred in a chromosomal region of zero-recombination
in the past at time x. Such a hitchhiking “catastrophe” wipes out completely genetic variation that existed in a population before that time. Standing
variation observed at present must therefore be due to mutations that have arisen since time point x. Assuming that all newly arising mutations are neutral, we derived expressions for the expectation, variance and also for
the higher moments of the number of nucleotide sites segregating in a sample of n genes as a function of x. The result for the first moment is then used to estimate the time back to the last hitchhiking event based on DNA polymorphism
data from Drosophila. Assuming that directional selection is the sole determinant of the level of genetic variation in the gene regions surveyed,
we obtained estimates of x that were typically in the order of 0.1N generations.
Received 14 May 1996; received in revised form 26 August 1996 相似文献
14.
Interaction of maturation delay and nonlinear birth in population and epidemic models 总被引:16,自引:0,他引:16
A population with birth rate function B(N) N and linear death rate for the adult stage is assumed to have a maturation delay T>0. Thus the growth equation N′(t)=B(N(t−T)) N(t−T) e−
d
1
T−dN(t) governs the adult population, with the death rate in previous life stages d
1≧0. Standard assumptions are made on B(N) so that a unique equilibrium N
e
exists. When B(N) N is not monotone, the delay T can qualitatively change the dynamics. For some fixed values of the parameters with d
1>0, as T increases the equilibrium N
e
can switch from being stable to unstable (with numerically observed periodic solutions) and then back to stable. When disease
that does not cause death is introduced into the population, a threshold parameter R
0 is identified. When R
0<1, the disease dies out; when R
0>1, the disease remains endemic, either tending to an equilibrium value or oscillating about this value. Numerical simulations
indicate that oscillations can also be induced by disease related death in a model with maturation delay.
Received: 2 November 1998 / Revised version: 26 February 1999 相似文献
15.
Genetic population structure of Japanese bagrid catfishes 总被引:3,自引:1,他引:2
The genetic population structures of four bagrid catfishes, allopatrically distributed in Japan, were investigated based
on nucleotide sequence data from the mitochondrial control region (ca. 420 bp) of 296 specimens from 29 river systems. Almost
no sequence variations were found within riverine populations of each species, especially Pseudobagrus ichikawai, in which no individual variations were found in any specimens from eight river systems throughout its range. In contrast,
the P. nudiceps population in the Lake Biwa–Yodo River system showed relatively high polymorphism. These results imply that the riverine
populations have undergone a bottleneck situation at some time. Most of the riverine populations of P. nudiceps and P. ichikawai, which are mainly distributed in areas around an inland sea or bay, were fixed into a single haplotype for each species.
On the other hand, in P. tokiensis and P. aurantiacus, which are distributed in areas surrounding extensive mountainous regions, the haplotype compositions clearly differed among
conspecific populations. These results suggest that some degree of gene flow existed among populations of each of the former
two species during glacial regression periods. Based on the genetic variability of P. fulvidraco, widely distributed in continental East Asia, and the degree of genetic divergence between P. aurantiacus and its possible sister species, P. taeniatus, in China, the evolutionary rate of East Asian bagrids appears to be relatively low, estimated at a few percent per million
years or less.
Received: June 5, 2002 / Revised: December 6, 2002 / Accepted: December 26, 2002 相似文献
16.
R. Finkeldey O. Murillo 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(3-4):664-668
The concept of the partitioning of genetic diversity into a component within and a component among populations (F
ST
- or G
ST
-statistics) can be easily expanded to compute the contribution of single subpopulations to total gene diversity. A subpopulation
contributes to total gene diversity with its single-population gene diversity plus the (weighted) mean of Nei’s minimum genetic
distances to all subpopulations. The suggested method allows one to unambiguously rank subpopulations according to the amount
they contribute to the total gene diversity. Genetic polymorphisms at four isozyme gene loci of Alnus acuminata in Costa Rica are used to illustrate the procedure and its biological interpretation.
Received: 15 August 1998 / Accepted: 8 September 1998 相似文献
17.
S. S. Papiha P. Amirshahi E. Sunderland D. D. Farhud S. H. Tavakoli P. Daneshmand 《International Journal of Anthropology》1992,7(3):11-18
The genetic structure of six populations of Iran (Turks, Kurds, Lurs, Zabolis, Baluchis and Zoroastrians) was examined using
data on blood groups, serum proteins and cell enzymes. Our results show conclusively that there are genetic differences among
the six populations and the analysis of superimposed R and S matrices defined Harpending & Jenkins (1973) show by that the
dispersion of some of the alleles correspond to the dispersion of the populations. The FST estimates are not large enough to favour selection on any of the loci studied. The FIT and FIS estimates are positive and moderately high suggesting that the genetic differentiation to some extent is influenced by inbreeding. 相似文献
18.
AFLP markers were used to investigate the population genetic differentiation among populations of Sebastes schlegelii from China and Japan. A total of 405 bands were amplified for 180 individuals from 9 populations by 3 pairs of selective primers. S. schlegelii exhibited high Nei's gene diversity with an average value of 0.29 for all populations. No significant genealogical branches or clusters corresponding to sampling localities were detected by UPGMA tree. The results of AMOVA analysis and pairwise FST values showed no genetic divergence among different geographic populations. The result of STRUCTURE demonstrated all populations of S. schlegelii examined in the study shared one single gene pool. 相似文献
19.
Thomas P. Witelski 《Journal of mathematical biology》1997,35(6):695-712
We study the qualitative properties of degenerate diffusion equations used to describe dispersal processes in population
dynamics. For systems of interacting populations, the forms of the diffusion models used determine if the population will
intermix or remain disjoint (segregated). The dynamics and stability of segregation boundaries between competing populations
is analyzed. General population models with segregation and mixing interactions are derived and connections to behavior in
fluid mechanical systems are addressed.
Received 19 January 1996; received in revised form 4 April 1996 相似文献
20.
Variation at seven microsatellite loci was investigated in three local E. alaskanus populations from Norway and microsatellite variation was compared with allozyme variation. The percentage of polymorphic
loci was 81%, the mean number of alleles per polymorphic locus was 5.7 and expected heterozygosity was 0.37. An F-statistic
analysis revealed an overall 48% deficit of heterozygotes over Hardy-Weinberg expectations. Gene diversity is mainly explained
by the within population component. The averaged between population differentiation coefficient, F
st
, over 7 loci is only 0.13, which accounts for only 13% of the whole diversity and was contrary to allozyme analysis. The
mean genetic distance between populations was 0.12. However, a χ2 -test showed that allele frequencies were different (p < 0.05) among the populations at 5 of the 7 loci. In comparison with
the genetic variation detected by allozymes, microsatellite loci showed higher levels of genetic variation. Microsatellite
analysis revealed that population H10576 possesses the lowest genetic variation among the tested three populations, which
concur with allozyme analysis. The dendrogram generated by microsatellites agreed very well with allozymic data. Our results
suggest that natural selection may be an important factor in shaping the genetic diversity in these three local E. alaskanus populations. Possible explanations for deficit heterozygosity and incongruence between microsatellites and allozymes are discussed.
Received November 6, 2001; accepted April 24, 2002 Published online: November 14, 2002
Addresses of the authors: Genlou Sun (e-mail: Genlou.sun@STMARYS.CA), Biology Department, Saint Mary's University, Halifax.
Nova Scotia, B3H 3C3, Canada. B. Salomon, R. von Bothmer, Department of Crop Science, The Swedish University of Agricultural
Sciences, P.O. Box 44, SE-230 53, Alnarp, Sweden. 相似文献