scholarly journals Molecular phylogeny and evolution of tropical vegetal genus Coccinia (Cucurbitaceae) using chloroplast barcode markers and its implications for speciation patterns

2017 ◽  
Vol 6 (12) ◽  
pp. 1817
Author(s):  
Mala Parab ◽  
Payel De ◽  
Sunita Singh
Keyword(s):  
Molecular Phylogeny ◽  
Population Analysis ◽  
Relative Rate ◽  
Bootstrap Method ◽  
Population Expansion ◽  
Land Races ◽  
Crop Development ◽  
Rate Test ◽  
Phylogeny And Evolution ◽  
Vegetatively Propagated Plants

Evaluation of molecular phylogeny employing barcode markers for a population analysis has revealed the association between character evolution and diversification. The present research study endeavors to estimate the molecular phylogeny and evolution amongst 30 geographically distant land races of Coccinia grandis using chloroplast barcode markers. On the basis of sequences of ­C. grandis landraces and sister genera’s of Cucurbits; phylogeny and evolutionary distances were estimated using bootstrap method of UPGMA and ML with MEGA and DAMBE software. The rbcL appear to be evolving marginally amongst land races studied, while matK loci exhibited several parsimonically insignificant variations. The ycf5 locus resolved efficiently the phylogeny at both intraspecies and intergeneric levels. The values of Tajima’s relative rate test, Nei’s genetic distance and gamma distribution, within C. grandis accessions and among Cucurbits denoted plausibility of occurrences of random population expansion, slow ontogenic transitions and high consanguinity percentage among core barcode regions.The present study thus lays a platform for researchers working with vegetatively propagated plants to plan strategies for exchange of varieties, their maintenance, utilization and enhancement for further crop development and propagation.

scholarly journals Analysis of substitution rates showed that TLR5 is evolving at different rates among mammalian groups

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Ana Pinheiro ◽  
Ana Águeda-Pinto ◽  
José Melo-Ferreira ◽  
Fabiana Neves ◽  
Joana Abrantes ◽  
...  
Keyword(s):  
Substitution Rate ◽  
Relative Rate ◽  
Purifying Selection ◽  
Genetic Distances ◽  
Major Protein ◽  
Substitution Rates ◽  
Evolutionary Pattern ◽  
Branch Model ◽  
Rate Test ◽  
Species Specific

Abstract Background Toll-like receptors (TLRs) are the most widely studied innate immunity receptors responsible for recognition of invading pathogens. Among the TLR family, TLR5 is the only that senses and recognizes flagellin, the major protein of bacterial flagella. TLR5 has been reported to be under overall purifying selection in mammals, with a small proportion of codons under positive selection. However, the variation of substitution rates among major mammalian groups has been neglected. Here, we studied the evolution of TLR5 in mammals, comparing the substitution rates among groups. Results In this study we analysed the TLR5 substitution rates in Euungulata, Carnivora, Chiroptera, Primata, Rodentia and Lagomorpha, groups. For that, Tajima’s relative rate test, Bayesian inference of evolutionary rates and genetic distances were estimated with CODEML’s branch model and RELAX. The combined results showed that in the Lagomorpha, Rodentia, Carnivora and Chiroptera lineages TLR5 is evolving at a higher substitution rate. The RELAX analysis further suggested a significant relaxation of selective pressures for the Lagomorpha (K = 0.22, p < 0.01), Rodentia (K = 0.58, p < 0.01) and Chiroptera (K = 0.65, p < 0.01) lineages and for the Carnivora ancestral branches (K = 0.13, p < 0.01). Conclusions Our results show that the TLR5 substitution rate is not uniform among mammals. In fact, among the different mammal groups studied, the Lagomorpha, Rodentia, Carnivora and Chiroptera are evolving faster. This evolutionary pattern could be explained by 1) the acquisition of new functions of TLR5 in the groups with higher substitution rate, i.e. TLR5 neofunctionalization, 2) by the beginning of a TLR5 pseudogenization in these groups due to some redundancy between the TLRs genes, or 3) an arms race between TLR5 and species-specific parasites.

Molecular phylogeny and evolution of the genus Neoerysiphe (Erysiphaceae, Ascomycota)

2008 ◽  
Vol 112 (6) ◽  
pp. 639-649 ◽  
Author(s):  
Susumu Takamatsu ◽  
Maria Havrylenko ◽  
Silvia M. Wolcan ◽  
Sanae Matsuda ◽  
Seiko Niinomi
Keyword(s):  
Molecular Phylogeny ◽  
Phylogeny And Evolution

Molecular phylogeny and evolution of Calaphidinae (Hemiptera: Aphididae)

Cladistics ◽  
2021 ◽  
Author(s):  
Yerim Lee ◽  
Mariusz Kanturski ◽  
Robert G. Foottit ◽  
Sora Kim ◽  
Seunghwan Lee
Keyword(s):  
Molecular Phylogeny ◽  
Phylogeny And Evolution

scholarly journals Research on Risk Measurement in Financial Market Based on GARCH-VaR and FHS——An Example of Chinese Bond Market

2018 ◽  
Vol 5 (4) ◽  
pp. 102
Author(s):  
Shaozhen Chen ◽  
Bangqian Zhang ◽  
Jinjin Deng
Keyword(s):  
Risk Management ◽  
Value At Risk ◽  
Bootstrap Method ◽  
Bond Market ◽  
Leverage Effect ◽  
Parameter Method ◽  
Historical Simulation ◽  
Rate Test ◽  
The Stability ◽  
T Distribution

Accurately measuring the risk of bond market is very important for improving the risk management level of bond market and maintaining the stability of the financial system. Taking ChinaBond New Composite Wealth (gross) Index as the research object, this paper selects the closing price from January 1, 2002 to March 30, 2018, establishes the GARCH, EGARCH and GJR-GARCH model based on normal distribution and t distribution, and finds out the volatility aggregation and the leverage effect of the bond market. Then, this paper use two methods  to measure the risk of the bond market: first, we estimate the value at risk (VaR) of the bond market by the parameter method, using conditional variance estimated by the GARCH models, and we carry out backtesting analysis and the Kupiec failure rate test on measurement accuracy of VaR. The results show that t distribution hypothesis and elimination of autocorrelation of the yield rate can improve the accuracy and robustness of the estimation of the VaR; second, we simulate the future revenue path of the bond market and compare it with the actual loss, using Filtered Historical Simulation (FHS) based on Bootstrap method. The results show that the bond market has leverage effect. The maximum possible loss under extreme conditions can be far greater than the maximum possible revenue. But the estimated VaR under 95% confidence level can predict future risks very well. Finally, according to the conclusion, this paper puts forward some suggestions for regulators and investors from the perspective of risk management.

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