scholarly journals Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

2017 ◽  
Author(s):  
Fiona M. Robertson ◽  
Manu Kumar Gundappa ◽  
Fabian Grammes ◽  
Torgeir R. Hvidsten ◽  
Anthony K. Redmond ◽  
...  
Keyword(s):  
Genome Duplication ◽  
Functional Divergence ◽  
Time Lag ◽  
Time Lags ◽  
Species Radiation ◽  
Evolutionary Diversification ◽  
Genome Wide ◽  
Physiological Adaptations ◽  
Lag Model ◽  
Functional Consequences

AbstractThe functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification is often highly temporally-detached from WGD. Salmonid fish, whose ancestor experienced WGD by autotetraploidization ~95 Ma (i.e. ‘Ss4R’), fit such a ‘time-lag’ model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model called ‘Lineage-specific Ohnologue Resolution’ (LORe) to address the phylogenetic and functional consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One quarter of each salmonid genome, harbouring at least 4,500 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions > 50 Myr post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that promoted salmonid species radiation. We show that LORe ohnologues are enriched for different functions than ‘older’ ohnologues that began diverging in the salmonid ancestor. LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear ‘explosively’, but can arise gradually over tens of Myr, promoting lineage-specific diversification regimes under prevailing ecological pressures.

scholarly journals Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon

2021 ◽  
Author(s):  
Jukka-Pekka Verta ◽  
Henry J Barton ◽  
Victoria Pritchard ◽  
Craig R Primmer
Keyword(s):  
Atlantic Salmon ◽  
Genetic Drift ◽  
Functional Divergence ◽  
Regulatory Elements ◽  
Functional Redundancy ◽  
Neutral Evolution ◽  
Whole Genome ◽  
Regulatory Evolution ◽  
Evolutionary Diversification ◽  
Genome Wide

Abstract Whole genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Mya. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained regulatory divergence. Patterns of genetic diversity across natural populations inferred from re-sequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift.

scholarly journals Molecular Polymorphism and Divergence of Duplicated Genes in Tetraploid African Clawed Frogs (Xenopus)

2015 ◽  
Vol 145 (3-4) ◽  
pp. 243-252 ◽  
Author(s):  
Ben J. Evans ◽  
Taejoon Kwon
Keyword(s):  
Genome Duplication ◽  
Gene Dosage ◽  
Functional Divergence ◽  
Single Copy ◽  
Duplicated Genes ◽  
Genetic Redundancy ◽  
Molecular Polymorphism ◽  
Genome Wide ◽  
Extant Species ◽  
Almost All

Genome duplication creates redundancy in proteins and their interaction networks, and subsequent smaller-scale gene duplication can further amplify genetic redundancy. Mutations then lead to the loss, maintenance or functional divergence of duplicated genes. Genome duplication occurred many times in African clawed frogs (genus Xenopus), and almost all extant species in this group evolved from a polyploid ancestor. To better understand the nature of selective constraints in a polyploid genome, we examined molecular polymorphism and divergence of duplicates and single-copy genes in 2 tetraploid African clawed frog species, Xenopus laevis and X. victorianus. We found that molecular polymorphism in the coding regions of putative duplicated genes was higher than in singletons, but not significantly so. Our findings also suggest that transcriptome evolution in polyploids is influenced by variation in the genome-wide mutation rate, and do not reject the hypothesis that gene dosage balance is also important.

scholarly journals Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Fiona M. Robertson ◽  
Manu Kumar Gundappa ◽  
Fabian Grammes ◽  
Torgeir R. Hvidsten ◽  
Anthony K. Redmond ◽  
...  
Keyword(s):  
Genome Duplication ◽  
Time Lags ◽  
Evolutionary Diversification

A distributed vaporization time-lag model for gas turbine combustor dynamics

1992 ◽  
Author(s):  
JAYESH MEHTA ◽  
P. MUNGUR ◽  
W. DODDS ◽  
L. DODGE
Keyword(s):  
Gas Turbine ◽  
Time Lag ◽  
Gas Turbine Combustor ◽  
Lag Model

scholarly journals In Vitro Model of Mycobacterial Growth Arrest Using Nitric Oxide with Limited Air

2008 ◽  
Vol 53 (1) ◽  
pp. 157-161 ◽  
Author(s):  
Syed Hussain ◽  
Muhammad Malik ◽  
Lanbo Shi ◽  
Maria Laura Gennaro ◽  
Karl Drlica
Keyword(s):  
Nitric Oxide ◽  
In Vitro Model ◽  
Transition Period ◽  
Time Lag ◽  
Growth Arrest ◽  
Ring Structure ◽  
Time Lags ◽  
Vitro Model ◽  
Mycobacterial Growth

ABSTRACT An in vitro model of mycobacterial growth arrest was developed using Mycobacterium bovis BCG. When an exponentially growing culture was transferred to an evacuated tube, growth continued; treatment with a source of nitric oxide (diethylenetriamine-nitric oxide adduct [DETA-NO] at 50 μM) halted growth immediately, and aeration restored growth. When the period of growth arrest exceeded 4 h, a time lag occurred before aeration could restore growth. The lag time was maximal (24 h) after 16 h of growth arrest. These time lags indicated that one transition period was required for cells to achieve full arrest of growth and another for them to recover fully from growth arrest. DETA-NO-induced growth arrest failed to protect from the lethal effects of anaerobic shock, which caused rapid lysis of both growing and growth-arrested cells. While growth arrest had little effect on the lethal action of rifampin, it eliminated isoniazid lethality. Growth arrest reduced but did not eliminate fluoroquinolone lethality. Two fluoroquinolones, moxifloxacin and gatifloxacin, were equally lethal to exponentially growing cells, but moxifloxacin was more active during growth arrest. This difference is attributed to the fluoroquinolone C-7 ring structure, the only difference between the compounds. Collectively these data characterize a new system for halting mycobacterial growth that may be useful for evaluating new antituberculosis agents.

IRREVERSIBLE INVESTMENT, OPERATING FLEXIBILITY, AND TIME LAGS

2010 ◽  
Vol 27 (02) ◽  
pp. 271-286 ◽  
Author(s):  
RYUTA TAKASHIMA ◽  
MAKOTO GOTO ◽  
MOTOH TSUJIMURA
Keyword(s):  
Time Lag ◽  
Peak Load ◽  
Price Volatility ◽  
Optimal Investment ◽  
Capacity Expansion ◽  
Fixed Cost ◽  
Time Lags ◽  
Investment Timing ◽  
Power Company ◽  
Optimal Investment Problem

We consider an optimal investment problem when a firm such as an electric power company has the operational flexibility to expand and contract capacity with fixed cost. This problem is formulated as an impulse control problem combined with optimal stopping. Consequently, we obtain optimal investment timing, optimal capacity expansion and contraction timing, and the investment value. We also show investment, capacity expansion and contraction rule are influenced by the price volatility and the initial capacity is also influenced by the ratio between base-load plant and peak-load plant. In addition, we investigate how time lag between investment and operation influences the investment rule.

scholarly journals Reconciling Lagrangian Diffusivity and Effective Diffusivity in Contour-Based Coordinates

2019 ◽  
Vol 49 (6) ◽  
pp. 1521-1539
Author(s):  
Yu-Kun Qian ◽  
Shiqiu Peng ◽  
Chang-Xia Liang
Keyword(s):  
Time Lag ◽  
Effective Diffusivity ◽  
Delta Function ◽  
Spreading Rate ◽  
Particle Dispersion ◽  
Small Scale ◽  
Time Lags ◽  
Conservative Tracer ◽  
Stirring Effect ◽  
Short Time

AbstractThe present study reconciles theoretical differences between the Lagrangian diffusivity and effective diffusivity in a transformed spatial coordinate based on the contours of a quasi-conservative tracer. In the transformed coordinate, any adiabatic stirring effect, such as shear-induced dispersion, is naturally isolated from diabatic cross-contour motions. Therefore, Lagrangian particle motions in the transformed coordinate obey a transformed zeroth-order stochastic (i.e., random walk) model with the diffusivity replaced by the effective diffusivity. Such a stochastic model becomes the theoretical foundation on which both diffusivities are exactly unified. In the absence of small-scale diffusion, particles do not disperse at all in the transformed contour coordinate. Besides, the corresponding Lagrangian autocorrelation becomes a delta function and is thus free from pronounced overshoot and negative lobe at short time lags that may be induced by either Rossby waves or mesoscale eddies; that is, particles decorrelate immediately and Lagrangian diffusivity is already asymptotic no matter how small the time lag is. The resulting instantaneous Lagrangian spreading rate is thus conceptually identical to the effective diffusivity that only measures the instantaneous irreversible mixing. In these regards, the present study provides a new look at particle dispersion in contour-based coordinates.

scholarly journals Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Tandem Repeats ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

scholarly journals Pointwise observation of the state given by complex time lag parabolic system

2017 ◽  
Vol 27 (1) ◽  
pp. 77-89
Author(s):  
Adam Kowalewski
Keyword(s):  
Boundary Condition ◽  
Parabolic System ◽  
Neumann Boundary Condition ◽  
Optimization Problems ◽  
Time Lag ◽  
Sufficient Conditions ◽  
Neumann Boundary ◽  
The State ◽  
Constant Time ◽  
Time Lags

AbstractVarious optimization problems for linear parabolic systems with multiple constant time lags are considered. In this paper, we consider an optimal distributed control problem for a linear complex parabolic system in which different multiple constant time lags appear both in the state equation and in the Neumann boundary condition. Sufficient conditions for the existence of a unique solution of the parabolic time lag equation with the Neumann boundary condition are proved. The time horizon T is fixed. Making use of the Lions scheme [13], necessary and sufficient conditions of optimality for the Neumann problem with the quadratic performance functional with pointwise observation of the state and constrained control are derived. The example of application is also provided.

scholarly journals Design of delay observer-based controllers for uncertain time-lag systems

1999 ◽  
Vol 5 (2) ◽  
pp. 121-137 ◽  
Author(s):  
Magdi S. Mahmoud ◽  
Mohamed Zribi
Keyword(s):  
Uncertain Systems ◽  
Closed Loop ◽  
Time Lag ◽  
Linear Matrix ◽  
Time Lags ◽  
Matrix Inequalities ◽  
Closed Loop System ◽  
Delayed Measurements ◽  
Uncertain Time ◽  
Theoretical Developments

In this paper, the problem of designing observers and observer-based controllers for a class of uncertain systems with input and state time lags is considered. We construct delay-type observers in which both the instantaneous as well as the delayed measurements are utilized. Using feedback control based on the reconstructed state, the behavior of the closed-loop system is investigated. It is established that the uncertain time-lag system with delay observer-based control is asymptotically stable. Expressions for the gain matrices are given based on two linear-matrix inequalities. A numerical example is given to illustrate the theoretical developments.

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