Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species)

2012 ◽  
Vol 65 (1) ◽  
pp. 203-212 ◽  
Author(s):  
W. Stewart Grant ◽  
Ming Liu ◽  
TianXiang Gao ◽  
Takashi Yanagimoto
Author(s):  
A. O. Marnila

Geragai graben is located in the South Sumatera Basin. It was formed by mega sequence tectonic process with various stratigraphic sequence from land and marine sedimentation. One of the overpressure indication zones in the Geragai graben is in the Gumai Formation, where the sedimentation is dominated by fine grained sand and shale with low porosity and permeability. The aim of the study is to localize the overpressure zone and to analyze the overpressure mechanism on the Gumai Formation. The Eaton method was used to determine pore pressure value using wireline log data, pressure data (RFT/FIT), and well report. The significant reversal of sonic and porosity log is indicating an overpressure presence. The cross-plot analysis of velocity vs density and fluid type data from well reports were used to analyze the causes of overpressure in the Gumai Formation. The overpressure in Gumai Formation of Geragai graben is divided into two zones, they are in the upper level and lower level of the Gumai Formation. Low overpressure have occurred in the Upper Gumai Formation and mild overpressure on the Lower Gumai Formation. Based on the analyzed data, it could be predicted, that the overpressure mechanism in the Upper Gumai Formation might have been caused by a hydrocarbon buoyancy, whereas in the Lower Gumai Formation, might have been caused by disequilibrium compaction as a result of massive shale sequence.


2018 ◽  
Vol 5 (04) ◽  
Author(s):  
SS SOLANKEY ◽  
ANIL K SINGH

Fifty one okra F1 hybrids (using 17 lines as female and 3 testers as male parent) were evaluated in RCBD design during two different consecutive seasons (summer and rainy). Phenotypic coefficient of variability (PCV) was higher than genotypic coefficient of variability (GCV) for all studied character exhibiting environmental effects on the expression of characters. Heritability (h2b) along with genetic advance per cent of mean was found highest for character YVMV (86.95% and 150.61%). All the 51 okra hybrids were grouped into 4 distinct clusters in which Cluster II was the largest cluster having 28 F1s (54.90% of total F1s) followed by Cluster I with 14 F1s (27.45% of total F1s). Out of the major 6 PCs, 4 principal components (PC1, PC2, PC3 and PC4) accounted with proportionate values of 22.61, 17.22, 11.87 and 10.63%, respectively and contributed 62.33 % of the cumulative variation having Eigen value more than one. Moreover, based on PCs and genetic divergence in Cluster I and Cluster IV for plant height, YVMV and number of fruit per plant is important to identify the best cross combination (Arka Abhay × Arka Anamika) in okra. Therefore, the best cross combinations for improvement in various economic traits can be recommended on the basis of genetic divergence and principal component analysis in okra.


Nature ◽  
1982 ◽  
Vol 295 (5845) ◽  
pp. 163-165 ◽  
Author(s):  
Stephen D. Ferris ◽  
Richard D. Sage ◽  
Allan C. Wilson

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Eleanor F. Miller ◽  
Andrea Manica

Abstract Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms’ classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species’ demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling. Results Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing sequence data for Bayesian skyline plot demographic reconstructions. Conclusions There is now more genetic information available than ever before and large meta-data sets offer great opportunities to explore new and exciting avenues of research. However, compiling multi-study datasets still remains a technically challenging prospect. The mtDNAcombine package provides a pipeline to streamline the process of downloading, curating, and analysing sequence data, guiding the process of compiling data sets from the online database GenBank.


Author(s):  
Thassya C. dos Santos Schmidt ◽  
Doug E. Hay ◽  
Svein Sundby ◽  
Jennifer A. Devine ◽  
Guðmundur J. Óskarsson ◽  
...  

AbstractLife-history traits of Pacific (Clupea pallasii) and Atlantic (Clupea harengus) herring, comprising both local and oceanic stocks subdivided into summer-autumn and spring spawners, were extensively reviewed. The main parameters investigated were body growth, condition, and reproductive investment. Body size of Pacific herring increased with increasing latitude. This pattern was inconsistent for Atlantic herring. Pacific and local Norwegian herring showed comparable body conditions, whereas oceanic Atlantic herring generally appeared stouter. Among Atlantic herring, summer and autumn spawners produced many small eggs compared to spring spawners, which had fewer but larger eggs—findings agreeing with statements given several decades ago. The 26 herring stocks we analysed, when combined across distant waters, showed clear evidence of a trade-off between fecundity and egg size. The size-specific individual variation, often ignored, was substantial. Additional information on biometrics clarified that oceanic stocks were generally larger and had longer life spans than local herring stocks, probably related to their longer feeding migrations. Body condition was only weakly, positively related to assumingly in situ annual temperatures (0–30 m depth). Contrarily, body growth (cm × y−1), taken as an integrator of ambient environmental conditions, closely reflected the extent of investment in reproduction. Overall, Pacific and local Norwegian herring tended to cluster based on morphometric and reproductive features, whereas oceanic Atlantic herring clustered separately. Our work underlines that herring stocks are uniquely adapted to their habitats in terms of trade-offs between fecundity and egg size whereas reproductive investment mimics the productivity of the water in question.


Plasma ◽  
2021 ◽  
Vol 4 (2) ◽  
pp. 239-251
Author(s):  
Masaomi Sanekata ◽  
Hiroshi Nishida ◽  
Tatsuya Watabe ◽  
Yuki Nakagomi ◽  
Yoshihiro Hirai ◽  
...  

Delayed discharges due to electrical breakdown are observed in modulated pulsed pow er magnetron sputtering (MPPMS) plasma of titanium. The delayed discharge, which is remarkable with decreasing argon gas pressure, transforms the discharge current waveform from a standard modulated pulsed discharge current waveform to a comb-like discharge current waveform consisting of several pulses with high power. In addition, the delay times, consisting of statistical times and formative times in the delayed MPPMS discharges, are experimentally measured with the help of Laue plot analysis. The pressure dependence of delay times observed indicates that the delayed discharge behavior matches the breakdown characteristics well. In the present study, the delayed discharge dynamics of the comb-like discharge current waveform, which can be the origin of deep oscillation magnetron sputtering, are investigated based on measurement of the delay times and the characteristics of discharge current waveforms.


Author(s):  
Martina Maria Calvino ◽  
Lorenzo Lisuzzo ◽  
Giuseppe Cavallaro ◽  
Giuseppe Lazzara ◽  
Stefana Milioto

AbstractIn this paper, films based on sustainable polymers with variable charge have been investigated by non-isothermal thermogravimetry in order to predict their lifetime, which is a key parameter for their potential use in numerous technological and biomedical applications. Specifically, chitosan has been selected as positively charged biopolymer, while alginate has been chosen as negatively charged biopolymer. Among non-ionic polymers, methylcellulose has been investigated. Thermogravimetric measurements at variable heating rates (5, 10, 15 and 20 °C min−1) have been performed for all the polymers to study their degradation kinetics by using isoconversional procedures combined with ‘Master plot’ analyses. Both integral (KAS and Starink methods) and differential (Friedman method) isoconversional procedures have shown that chitosan possesses the highest energetic barrier to decomposition. Based on the Master plot analysis, the decomposition of ionic polymers can be described by the R2 kinetic model (contracted cylindrical geometry), while the degradation of methylcellulose reflects the D2 mechanism (two-dimensional diffusion). The determination of both the decomposition mechanism and the kinetic parameters (activation energy and pre-exponential factor) has been used to determine the decay time functions of the several biopolymers. The obtained insights can be helpful for the development of durable films based on sustainable polymers with variable electrostatic characteristics. Graphical abstract


Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3930
Author(s):  
Salvatore Giovanni De-Simone ◽  
Guilherme Curty Lechuga ◽  
Paloma Napoleão-Pêgo ◽  
Larissa Rodrigues Gomes ◽  
David William Provance ◽  
...  

Introduction: Snakebite envenomation is considered a neglected tropical disease, and SVTLEs critical elements are involved in serious coagulopathies that occur on envenoming. Although some enzymes of this group have been structurally investigated, it is essential to characterize other proteins to better understand their unique properties such as the Lachesis muta rhombeata 47 kDa (Lmr-47) venom serine protease. Methods: The structure of Lmr-47 was studied in solution, using SAXS, DLS, CD, and in silico by homology modeling. Molecular docking experiments simulated 21 competitive inhibitors. Results: At pH 8.0, Lmr-47 has an Rg of 34.5 ± 0.6 Å, Dmax of 130 Å, and SR of 50 Å, according to DLS data. Kratky plot analysis indicates a rigid shape at pH 8.0. Conversely, the pH variation does not change the center of mass’s intrinsic fluorescence, possibly indicating the absence of fluorescent amino acids in the regions affected by pH variation. CD experiments show a substantially random coiled secondary structure not affected by pH. The low-resolution model of Lmr-47 presented a prolate elongated shape at pH 8.0. Using the 3D structure obtained by molecular modeling, docking experiments identified five good and three suitable competitive inhibitors. Conclusion: Together, our work provided insights into the structure of the Lmr-47 and identified inhibitors that may enhance our understanding of thrombin-like family proteins.


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