scholarly journals POPULATION BOTTLENECKS AND NONEQUILIBRIUM MODELS IN POPULATION GENETICS. III. GENIC HOMOZYGOSITY IN POPULATIONS WHICH EXPERIENCE PERIODIC BOTTLENECKS

Genetics ◽  
1985 ◽  
Vol 111 (3) ◽  
pp. 691-703
Author(s):  
Takeo Maruyama ◽  
Paul A Fuerst
Keyword(s):  
Population Size ◽  
Cycle Length ◽  
Extreme Values ◽  
Gene Diversity ◽  
Population Bottlenecks ◽  
Specific Time ◽  
Large Gene ◽  
Analytical Formulas ◽  
Two Phases ◽  
Two Parameters

ABSTRACT The amount of variability in a population that experiences repeated restrictions in population size has been calculated. The restrictions in size occur cyclically with a fixed cycle length. Analytical formulas for describing the gene identity at any specific time in the expanded and restricted phases of the cycle, and for the average and second moment of the gene identity, have been derived. It is shown that the level of genetic diversity depends critically on the two parameters that account for the population size, mutation rate and the time of duration for each of the two phases in the cycle. If one or both of these composite parameters are small, the gene diversity will be much reduced, and population gene diversity will then be predictable from knowledge of the harmonic mean population size over the entire cycle. If these parameters take on intermediate values, diversity changes constantly during the cycle, fluctuating steadily from a high to a low value and back again. If these parameters are large, gene diversity will fluctuate rapidly between extreme values and will stay at the extremes for long periods of time.

Genetic Diversity among Calamus brandisii Becc. (Arecaceae) Populations in Kerala Part of Western Ghats

2021 ◽  
Vol 43 (1) ◽  
pp. 38-42
Author(s):  
Kavungal Priya ◽  
◽  
Indira . ◽  
Vadakkethil Balakrishnan Sreekumar ◽  
Renuka . ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Western Ghats ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Issr Markers ◽  
High Genetic Diversity ◽  
Western Ghats Of India ◽  
The Mean ◽  
Two Parameters ◽  
Two Populations

Calamus brandisii Becc. is one of the endemic slender rattans found in the Western Ghats of India. The genetic diversity of two main populations available in Kerala was investigated using 20 RAPD and 9 ISSR markers. Two parameters viz., gene diversity and genetic diversity within and among populations were analyzed. ISSR analysis showed quite high genetic diversity in Pandimotta compared to Bonacaud population whereas in RAPD markers both these populations were moderately diverse. The percentage of total genetic differentiation (Gst) among two populations is relatively higher than the mean Gst value indicating high genetic diversity within the populations. The genetic distance between these two populations was 0.1739 with ISSR markers and 0.1971 with RAPD markers. Because of its high genetic diversity, Pandimotta population can be treated as an important population of gene diversity with potentially useful genes. This may be included in the high priority reservoir for genetic conservation also.

scholarly journals Analytical Design of the Human Bronchial Tree for Healthy Patients and Patients with Obstructive Pulmonary Diseases

2019 ◽  
Vol 14 (2) ◽  
pp. 635-648 ◽  
Author(s):  
A.E. Medvedev ◽  
P.S. Gafurova
Keyword(s):  
Airway Obstruction ◽  
Bronchial Tree ◽  
Pulmonary Diseases ◽  
Cylindrical Shape ◽  
Analytical Design ◽  
Geometric Characteristics ◽  
Analytical Formulas ◽  
Two Parameters ◽  
Pathological Case ◽  
Order Smoothness

The study is aimed at the analytical design of the full human bronchial tree for healthy patients and patients with obstructive pulmonary diseases. Analytical formulas for design of the full bronchial tree are derived. All surfaces of the bronchial tree are matched with the second-order smoothness (there are no acute angles or ribs). The geometric characteristics of the human bronchial tree in the pathological case are modeled by a “starry” shape of the inner structure of the bronchus; the pathology degree is defined by two parameters: bronchus constriction level and degree of distortion of the cylindrical shape of the bronchus. Closed analytical formulas allow the human bronchial tree of an arbitrary complexity (up to alveoli) to be designed; moreover, the parametric dependences make it possible to specify any desirable degree of airway obstruction.

Changes in nucleoli and nucleolar fibrillar centres of chromaffin cells in rat adrenal medulla over a 24-hour period: an ultrastructural and stereological analysis

1985 ◽  
Vol 77 (1) ◽  
pp. 255-262
Author(s):  
A. Robaglia ◽  
R. Seite
Keyword(s):  
Adrenal Medulla ◽  
Chromaffin Cells ◽  
Extreme Values ◽  
Sympathetic Neurons ◽  
Cellular Level ◽  
Temporal Organization ◽  
Free Access ◽  
Stereological Analysis ◽  
The Mean ◽  
Two Parameters

A stereological and ultrastructural study was performed on the nucleoli of the adrenal medulla chromaffin cells of rats exposed to a standardized 12 h light/12 h dark cycle with free access to food and water. The animals were killed three at a time, every 4 h during the 24-h span and fixed by intracardiac perfusion. In these reticulated nucleoli, the stereological analysis over a 24-h period showed a variation dependent on the time of killing for the two parameters investigated, the mean nucleolar volume, Vnu, and the mean volume of the fibrillar centres, Vfc(nu). The minimal value occurred at 0300 h (dark span) and the maximal one at 0700 h (at the onset of the light span). Between these two extreme values, Vnu increased 1.8-fold and Vfc(nu) 5.3-fold. These data are compared with a previous description from our laboratory of circadian rhythm in nucleoli of sympathetic neurons of superior cervical ganglion in the same animals. Analogies and differences are pointed out, but apart from these considerations the present study provides a new example of temporal organization at the cellular level in the organelle involved in ribosomal RNA synthesis and ribosome assembly.

scholarly journals Choosing Mutation and Crossover Ratios for Genetic Algorithms—A Review with a New Dynamic Approach

Information ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 390 ◽  
Author(s):  
Ahmad Hassanat ◽  
Khalid Almohammadi ◽  
Esra’a Alkafaween ◽  
Eman Abunawas ◽  
Awni Hammouri ◽  
...  
Keyword(s):  
Population Size ◽  
Optimization Problems ◽  
Large Population ◽  
Small Population ◽  
Mutation Rates ◽  
Mutation Operators ◽  
Tuning Methods ◽  
Two Parameters ◽  
The Impact ◽  
Crossover And Mutation

Genetic algorithm (GA) is an artificial intelligence search method that uses the process of evolution and natural selection theory and is under the umbrella of evolutionary computing algorithm. It is an efficient tool for solving optimization problems. Integration among (GA) parameters is vital for successful (GA) search. Such parameters include mutation and crossover rates in addition to population that are important issues in (GA). However, each operator of GA has a special and different influence. The impact of these factors is influenced by their probabilities; it is difficult to predefine specific ratios for each parameter, particularly, mutation and crossover operators. This paper reviews various methods for choosing mutation and crossover ratios in GAs. Next, we define new deterministic control approaches for crossover and mutation rates, namely Dynamic Decreasing of high mutation ratio/dynamic increasing of low crossover ratio (DHM/ILC), and Dynamic Increasing of Low Mutation/Dynamic Decreasing of High Crossover (ILM/DHC). The dynamic nature of the proposed methods allows the ratios of both crossover and mutation operators to be changed linearly during the search progress, where (DHM/ILC) starts with 100% ratio for mutations, and 0% for crossovers. Both mutation and crossover ratios start to decrease and increase, respectively. By the end of the search process, the ratios will be 0% for mutations and 100% for crossovers. (ILM/DHC) worked the same but the other way around. The proposed approach was compared with two parameters tuning methods (predefined), namely fifty-fifty crossover/mutation ratios, and the most common approach that uses static ratios such as (0.03) mutation rates and (0.9) crossover rates. The experiments were conducted on ten Traveling Salesman Problems (TSP). The experiments showed the effectiveness of the proposed (DHM/ILC) when dealing with small population size, while the proposed (ILM/DHC) was found to be more effective when using large population size. In fact, both proposed dynamic methods outperformed the predefined methods compared in most cases tested.

scholarly journals Models of long term artificial selection in finite population

1986 ◽  
Vol 48 (1) ◽  
pp. 41-50 ◽  
Author(s):  
William G. Hill ◽  
Jonathan Rasbash
Keyword(s):  
Population Size ◽  
Frequency Distribution ◽  
Selection Response ◽  
Initial Distribution ◽  
Gene Frequencies ◽  
Frequency Distributions ◽  
Gene Effect ◽  
Wide Range ◽  
Breeding Programmes ◽  
Two Parameters

SummaryThe effects of population size and selection intensity, which are in the breeder's control, are investigated for ranges of values of quantities outside his control, namely the number, initial distribution of frequencies and effects of genes influencing the trait. Two alleles are assumed to be initially segregating at each locus, with no linkage, dominance or epistasis. The effects are assumed to follow a gamma distribution, using a wide range of its two parameters which specify both mean gene effect or selective value and the shape of the distribution, or the ratio of Wright's effective number to actual number of genes. The initial gene frequencies (q) are assumed to be either 0·5 at all loci, uniformly distributed over the range 0–1, or to have a U-shaped distribution, proportional to [q(1 − q)]−1 such as derives from neutral mutation, with gene effect and frequency distributions independent. The mean and variance of selection response and limits, in the absence of new mutation, are derived.The shape of the distribution of effects is not usually important even up to the selection limit. With appropriate parametrization, the influence of the initial frequency distribution is small over a wide range of parameters. For reasonable choices of parameters, the effects of changing population size from those typically used in animal breeding programmes are likely to be small, but not negligible. For the initial U-shaped frequency distribution, further increases in population size are always expected to give a greater limit, regardless of present value, but not for the other distributions.

scholarly journals Multilocus Diversity in an Outbreeding Weed, Echium piantagineum L.

1983 ◽  
Vol 36 (6) ◽  
pp. 503 ◽  
Author(s):  
AHD Brown ◽  
JJ Burdon
Keyword(s):  
Biological Control ◽  
Linkage Disequilibrium ◽  
Genetic Structure ◽  
Population Size ◽  
Gene Diversity ◽  
Genotypic Variation ◽  
Vast Array ◽  
Multilocus Genotypes ◽  
Isozyme Loci

A population of E. plantagineum was surveyed for its genetic structure at 23 isozyme loci. More than half (13) of these loci were polymorphic, with an average number of three alleles per locus, a gene diversity of 38% and heterozygosity of 35%. More importantly, the distribution of multilocus heterozygosity over individuals was found to approximate that assuming independence among loci or no linkage disequilibrium. The population consisted of a vast array of multilocus genotypes. This pattern indicates that the outbreeding system encourages recombination sufficient to outweigh the effects on multilocus structure of bottlenecks in population size. Genic and genotypic variation presumably allows high levels of biochemical flexibility in populations of E. plantagineum. Such flexibility could hamper attempts at biological control.

scholarly journals POPULATION BOTTLENECKS AND NONEQUILIBRIUM MODELS IN POPULATION GENETICS. I. ALLELE NUMBERS WHEN POPULATIONS EVOLVE FROM ZERO VARIABILITY

Genetics ◽  
1984 ◽  
Vol 108 (3) ◽  
pp. 745-763
Author(s):  
Takeo Maruyama ◽  
Paul A Fuerst
Keyword(s):  
Gene Diversity ◽  
Population Expansion ◽  
Allele Frequency Distribution ◽  
Population Bottlenecks ◽  
Rare Alleles ◽  
The Mean ◽  
Low Levels ◽  
Short Time ◽  
Initial Distributions ◽  
Sudden Population Expansion

ABSTRACT A simple numerical method was developed for the mean number and average age of alleles in a population that was initiated with no genetic variation following a sudden population expansion. The methods are used to examine the question of whether allele numbers are elevated compared with values seen in equilibrium populations having equivalent gene diversity. Excess allele numbers in expanding populations were found to be the rule. This was true whether the population began with zero variation or with low levels of variation in either of two initial distributions (initially an equilibrium allele frequency distribution or initially with loci occurring in only two classes of variation). Although the increase of alleles may persist for only a short time, when compared with the time which is required for approach to final equilibrium, the increase may be long when measured in absolute generation numbers. The pattern of increase in very rare alleles (those present only once in a sample) and the persistence of the original allele were also investigated.

scholarly journals Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease

2021 ◽  
Vol 17 (1) ◽  
pp. e1009254
Author(s):  
Wei Wang ◽  
Duo Peng ◽  
Rodrigo P. Baptista ◽  
Yiran Li ◽  
Jessica C. Kissinger ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Immune Responses ◽  
Gene Amplification ◽  
Gene Diversity ◽  
Gene Families ◽  
Copy Number Variations ◽  
Host Immune Responses ◽  
Large Gene ◽  
Genes Encoding ◽  
Long Read

The protozoan Trypanosoma cruzi almost invariably establishes life-long infections in humans and other mammals, despite the development of potent host immune responses that constrain parasite numbers. The consistent, decades-long persistence of T. cruzi in human hosts arises at least in part from the remarkable level of genetic diversity in multiple families of genes encoding the primary target antigens of anti-parasite immune responses. However, the highly repetitive nature of the genome–largely a result of these same extensive families of genes–have prevented a full understanding of the extent of gene diversity and its maintenance in T. cruzi. In this study, we have combined long-read sequencing and proximity ligation mapping to generate very high-quality assemblies of two T. cruzi strains representing the apparent ancestral lineages of the species. These assemblies reveal not only the full repertoire of the members of large gene families in the two strains, demonstrating extreme diversity within and between isolates, but also provide evidence of the processes that generate and maintain that diversity, including extensive gene amplification, dispersion of copies throughout the genome and diversification via recombination and in situ mutations. Gene amplification events also yield significant copy number variations in a substantial number of genes presumably not required for or involved in immune evasion, thus forming a second level of strain-dependent variation in this species. The extreme genome flexibility evident in T. cruzi also appears to create unique challenges with respect to preserving core genome functions and gene expression that sets this species apart from related kinetoplastids.

Under what conditions do climatic variations lead to incision of alluvial fans? Insights from coupled catchment-fan system in the lab

2021 ◽  
Author(s):  
Stéphane Bonnet ◽  
Valeria Zavala-Ortiz ◽  
Sébastien Carretier
Keyword(s):  
Extreme Values ◽  
Laser Sheet ◽  
Sediment Concentration ◽  
Precipitation Rate ◽  
Dynamic State ◽  
Alluvial Fans ◽  
Equilibrium Degree ◽  
Artificial Rainfall ◽  
Arid Condition ◽  
Two Parameters

<p>Although a transition from aggradation to incision is observed in many natural alluvial fans and is usually related to variations in climate, the condition driving such change remain unclear. We address this problem here by considering laboratory experiments of coupled catchment-fans systems forced by oscillatory precipitation. In the 8 experiments considered here, eroded materials from an uplifting mountain may deposit on a plateau, erosion being driven by the surface runoff of water from an artificial rainfall device. These experiments, 700 to 900 minutes-long, were performed with the same uplift rate but with different sequences of variations of the rainfall rate (10 to 40 minutes-long) between two extreme values. The topography was digitized every 10 minutes thanks to a high-resolution laser sheet.</p><p>We observe that the sediment (Qs) and water (Qw) fluxes at the outlet of mountain catchments continuously vary with time, not only because of precipitation oscillations but also because of the dynamic state of the landscape. For a given precipitation rate, variations of Qs and Qw depend on whether the catchments enlarge or shrink, with additional variations of Qs depending on the equilibrium degree (steady-state or not). Depending on these conditions, we document a large variety of trends of Qs vs Qw in rivers at catchment outlets, Qs increasing or decreasing with Qw, or being independent of Qw. For a given catchment, oscillations in precipitation rate then drive alternations between two individual Qs vs Qw trends, the slope of these trends being indicative of the sediment concentration in the mini-rivers at the outlet of catchments that feed alluvial fans.</p><p>Our experiments indicate that incision of alluvial fans is controlled by two necessary conditions. First, it occurs when rainfall increases and goes with a decrease of the Qs/Qw ratio, i.e. with a decrease of concentration at the outlet of the catchment. Second, this control is modulated by the slope of the fan, incision only occurring for fans above a threshold slope. Then, the decrease in sediment concentration required to initiate the incision is weak for steeper fans, those that developed under a mean dry climate. A larger drop in concentration is necessary for gentle fans, those that develop under a mean wetter climate.</p><p>Several studies already demonstrated how a decrease of Qs or an increase of Qw drives incision. We show here that these two parameters are also coupled and covariate following the dynamical state of catchments. We also demonstrate that the decrease of the Qs/Qw ratio required for initiating the incision of a fan is lower for steeper fans, that is for fans that develop under more arid condition.</p><p>We conclude that a given amplitude of climate change won’t have the same imprint on landscapes, erosion and transport depending on the mean prevailing climate.</p>

Sign in / Sign up

Export Citation Format

Share Document