Simultaneous enhancement of multiple stability properties using two-parameter control methods inDrosophila melanogaster

2015 ◽  
Author(s):  
Sudipta Tung ◽  
Abhishek Mishra ◽  
Sutirth Dey
Keyword(s):  
Parameter Control ◽  
Population Fluctuations ◽  
Control Methods ◽  
Effective Population ◽  
Linear Dynamics ◽  
Wide Range ◽  
Population Sizes ◽  
Almost All ◽  
Two Parameter ◽  
Multiple Stability

Although a large number of methods have been proposed to control the non-linear dynamics of unstable populations, very few have been actually adopted for application. One reason for this gap is the fact that few control methods have been empirically verified using biological populations. To address this issue, we investigated the effects of two well-studied control methods (Both Limiter Control and Target-Oriented Control) on the dynamics of unstable populations ofDrosophila melanogaster. We show that both methods can significantly reduce population fluctuations, decrease extinction probability and increase effective population size simultaneously. This is in contrast with single parameter control methods that are not able to achieve multiple aspects of stability at the same time. We use the distribution of population sizes to derive biologically intuitive explanations for the mechanisms of how these two control methods attain stability. Finally, we show that non-Drosophila specific biologically realistic simulations are able to capture almost all the trends of our data. This shows that our results are likely generalizable over a wide range of taxa. The primary insight of our study is that control methods that incorporate both culling and restocking have better all-round performance in terms of stabilizing populations.

scholarly journals Stabilizing the dynamics of laboratory populations ofDrosophila melanogasterthrough upper and lower limiter controls

2015 ◽  
Author(s):  
Sudipta Tung ◽  
Abhishek Mishra ◽  
Sutirth Dey
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Real Life ◽  
Extinction Probability ◽  
Population Fluctuations ◽  
Control Methods ◽  
Effective Population ◽  
Population Dynamics Model ◽  
Wide Range ◽  
Laboratory Populations

Although a large number of methods exist to control the dynamics of populations to a desired state, few of them have been empirically validated. This limits the scope of using these methods in real-life scenarios. To address this issue, we tested the efficacy of two well-known control methods in enhancing different kinds of stability in highly fluctuating, extinction-prone populations ofDrosophila melanogaster. The Upper Limiter Control (ULC) method was able to reduce the fluctuations in population sizes as well as the extinction probability of the populations. On the negative side, it had no effect on the effective population size and required a large amount of effort. On the other hand, Lower Limiter Control (LLC) enhanced effective population size and reduced extinction probability at a relatively low amount of effort. However, its effects on population fluctuations were equivocal. We examined the population size distributions with and without the control methods, to derive biologically intuitive explanations for how these control methods work. We also show that biologically-realistic simulations, using a very general population dynamics model, are able to capture most of the trends of our data. This suggests that our results are likely to be generalizable to a wide range of scenarios.

scholarly journals Unbiased Estimation of Linkage Disequilibrium from Unphased Data

2019 ◽  
Vol 37 (3) ◽  
pp. 923-932 ◽  
Author(s):  
Aaron P Ragsdale ◽  
Simon Gravel
Keyword(s):  
Linkage Disequilibrium ◽  
Unbiased Estimation ◽  
Sequencing Data ◽  
Effective Population ◽  
Island Fox ◽  
Wide Range ◽  
Population Sizes ◽  
The Common ◽  
Genomic Regions ◽  
The Relationship

Abstract Linkage disequilibrium (LD) is used to infer evolutionary history, to identify genomic regions under selection, and to dissect the relationship between genotype and phenotype. In each case, we require accurate estimates of LD statistics from sequencing data. Unphased data present a challenge because multilocus haplotypes cannot be inferred exactly. Widely used estimators for the common statistics r2 and D2 exhibit large and variable upward biases that complicate interpretation and comparison across cohorts. Here, we show how to find unbiased estimators for a wide range of two-locus statistics, including D2, for both single and multiple randomly mating populations. These unbiased statistics are particularly well suited to estimate effective population sizes from unlinked loci in small populations. We develop a simple inference pipeline and use it to refine estimates of recent effective population sizes of the threatened Channel Island Fox populations.

scholarly journals Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size

2021 ◽  
Author(s):  
Michaela Halsey ◽  
John Stuhler ◽  
Natalia J Bayona-Vasquez ◽  
Roy N Platt ◽  
Jim R Goetze ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Population Fluctuations ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Single Nucleotide ◽  
Demographic Dynamics ◽  
Population Sizes

Organisms with low effective population sizes are at greater risk of extinction because of reduced genetic diversity.   Dipodomys elator  is a kangaroo rat that is classified as threatened in Texas and field surveys from the past 50 years indicate that the distribution of this species has decreased. This suggests geographic range reductions that could have caused population fluctuations, potentially impacting effective population size. Conversely, the more common and widespread  D. ordii  is thought to exhibit relative geographic and demographic stability. Genetic variation between  D. elator  and  D. ordii  samples was assessed using 3RAD, a modified restriction site associated sequencing approach. It was hypothesized that  D. elator  would show lower levels of nucleotide diversity, observed heterozygosity, and effective population size when compared to  D. ordii . Also of interest was identifying population structure within contemporary samples of  D. elator  and detecting genetic variation between temporal samples that could indicate demographic dynamics. Up to 61,000 single nucleotide polymorphisms were analyzed. It was determined that genetic variability and effective population size in contemporary  D. elator  populations were lower than that of  D. ordii, that there is only slight, if any, structure within contemporary  D. elator  populations, and there is little genetic differentiation between spatial or temporal historical samples suggesting little change in nuclear genetic diversity over 30 years. Results suggest that genetic diversity of  D. elator  has remained stable despite claims of reduced population size and/or abundance, which may indicate a metapopulation-like system, whose fluctuations might counteract any immediate decrease in fitness.

The Nonadaptive Forces of Evolution

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Recombination Rate ◽  
Effective Population ◽  
Evolutionary Forces ◽  
Wide Range ◽  
Population Sizes ◽  
Genomic Results

This chapter examines the relative strengths of the nonadaptive evolutionary forces (drift, mutation, recombination) acting on genomes. It reviews estimators for effective population size, mutation rate, and recombination rate, and summarizes the known genomic results over a wide range of taxa. The mutation rate tends to be lower in organisms with larger effective population sizes, consistent with the drift-barrier hypothesis wherein selection is ineffective when it is less than the reciprocal of the effective population size.

scholarly journals Evolution of Codon Usage Bias in Diatoms

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 894 ◽  
Author(s):  
Marc Krasovec ◽  
Dmitry A. Filatov
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Bias ◽  
Diatom Species ◽  
Effective Population ◽  
Weak Selection ◽  
Optimal Codons ◽  
Wide Range ◽  
Population Sizes ◽  
Selection For

Codon usage bias (CUB)—preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. CUB is thought to be caused by weak selection for translational accuracy and efficiency. Weak selection can overpower genetic drift only in species with large effective population sizes, such as Drosophila that has relatively strong CUB, while organisms with smaller population sizes (e.g., mammals) have weak CUB. Marine plankton species tend to have extremely large populations, suggesting that CUB should be very strong. Here we test this prediction and describe the patterns of codon usage in a wide range of diatom species belonging to 35 genera from 4 classes. We report that most of the diatom species studied have surprisingly modest CUB (mean Effective Number of Codons, ENC = 56), with some exceptions showing stronger codon bias (ENC = 44). Modest codon bias in most studied diatom species may reflect extreme disparity between astronomically large census and modest effective population size (Ne), with fluctuations in population size and linked selection limiting long-term Ne and rendering selection for optimal codons less efficient. For example, genetic diversity (pi ~0.02 at silent sites) in Skeletonema marinoi corresponds to Ne of about 10 million individuals, which is likely many orders of magnitude lower than its census size. Still, Ne ~107 should be large enough to make selection for optimal codons efficient. Thus, we propose that an alternative process—frequent changes of preferred codons, may be a more plausible reason for low CUB despite highly efficient selection for preferred codons in diatom populations. The shifts in the set of optimal codons should result in the changes of the direction of selection for codon usage, so the actual codon usage never catches up with the moving target of the optimal set of codons and the species never develop strong CUB. Indeed, we detected strong shifts in preferential codon usage within some diatom genera, with switches between preferentially GC-rich and AT-rich 3rd codon positions (GC3). For example, GC3 ranges from 0.6 to 1 in most Chaetoceros species, while for Chaetoceros dichaeta GC3 = 0.1. Both variation in selection intensity and mutation spectrum may drive such shifts in codon usage and limit the observed CUB. Our study represents the first genome-wide analysis of CUB in diatoms and the first such analysis for a major phytoplankton group.

First Detection of Tobacco Mosaic Virus in Tobacco Fields in Northern Lebanon

2020 ◽  
Vol 20 ◽  
Author(s):  
Rami Obeid ◽  
Elias Wehbe ◽  
Mohamad Rima ◽  
Mohammad Kabara ◽  
Romeo Al Bersaoui ◽  
...  
Keyword(s):  
Tobacco Mosaic Virus ◽  
Mosaic Virus ◽  
Viral Genome ◽  
Virus Genome ◽  
Enzyme Linked Immunosorbent Assay ◽  
Virus Family ◽  
Crop Fields ◽  
Wide Range ◽  
Almost All ◽  
Das Elisa

Background: Tobacco mosaic virus (TMV) is the most known virus in the plant mosaic virus family and is able to infect a wide range of crops, in particularly tobacco, causing a production loss. Objectives: Herein, and for the first time in Lebanon, we investigated the presence of TMV infection in crops by analyzing 88 samples of tobacco, tomato, cucumber and pepper collected from different regions in North Lebanon. Methods: Double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), revealed a potential TMV infection of four tobacco samples out of 88 crops samples collected. However, no tomato, cucumber and pepper samples were infected. The TMV+ tobacco samples were then extensively analyzed by RT-PCR to detect viral RNA using different primers covering all the viral genome. Results and Discussion: PCR results confirmed those of DAS-ELISA showing TMV infection of four tobacco samples collected from three crop fields of North Lebanon. In only one of four TMV+ samples, we were able to amplify almost all the regions of viral genome, suggesting possible mutations in the virus genome or an infection with a new, not yet identified, TMV strain. Conclusion: Our study is the first in Lebanon revealing TMV infection in crop fields, and highlighting the danger that may affect the future of agriculture.

INFLUENCE OF WEATHER ON TEMPORARY AND PERMANENT MIGRATION IN RURAL INDIA

2013 ◽  
Vol 04 (02) ◽  
pp. 1350007 ◽  
Author(s):  
K. S. KAVI KUMAR ◽  
BRINDA VISWANATHAN
Keyword(s):  
National Sample ◽  
Sample Survey ◽  
Urban Migration ◽  
Temporary Migration ◽  
Urban Migrants ◽  
Wide Range ◽  
Permanent Migration ◽  
Sample Survey Data ◽  
Almost All ◽  
Temporary Migrants

While a wide range of factors influence rural–rural and rural–urban migration in developing countries, there is significant interest in analyzing the role of agricultural distress and growing inter-regional differences in fueling such movement. This strand of research acquires importance in the context of climate change adaptation. In the Indian context, this analysis gets further complicated due to the significant presence of temporary migration. This paper analyzes how weather and its variability affects both temporary and permanent migration in India using National Sample Survey data for the year 2007–2008. The paper finds that almost all of the rural–urban migrants are permanent. Only temperature plays a role in permanent migration. In contrast, many temporary migrants are rural–rural and both temperature and rainfall explain temporary migration.

scholarly journals EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON SHORT-TERM RESPONSE TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽  
1973 ◽  
Vol 73 (3) ◽  
pp. 513-530
Author(s):  
J P Hanrahan ◽  
E J Eisen ◽  
J E Legates
Keyword(s):  
Population Size ◽  
Selection Response ◽  
Selection Intensity ◽  
Realized Heritability ◽  
Family Selection ◽  
Effective Population ◽  
Population Sizes ◽  
Selection For ◽  
Selection Intensities ◽  
Term Response

ABSTRACT The effects of population size and selection intensity on the mean response was examined after 14 generations of within full-sib family selection for postweaning gain in mice. Population sizes of 1, 2, 4, 8 and 16 pair matings were each evaluated at selection intensities of 100% (control), 50% and 25% in a replicated experiment. Selection response per generation increased as selection intensity increased. Selection response and realized heritability tended to increase with increasing population size. Replicate variability in realized heritability was large at population sizes of 1, 2 and 4 pairs. Genetic drift was implicated as the primary factor causing the reduced response and lowered repeatability at the smaller population sizes. Lines with intended effective population sizes of 62 yielded larger selection responses per unit selection differential than lines with effective population sizes of 30 or less.

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