scholarly journals A Bayesian Approach for Inferring the Impact of a Discrete Character on Rates of Continuous-Character Evolution in the Presence of Background-Rate Variation

2019 ◽  
Vol 69 (3) ◽  
pp. 530-544 ◽  
Author(s):  
Michael R May ◽  
Brian R Moore
Keyword(s):  
Bayesian Approach ◽  
Null Model ◽  
Character Evolution ◽  
Rate Variation ◽  
Background Rate ◽  
Dependent Rate ◽  
State Dependent ◽  
Discrete Character ◽  
The Impact ◽  
Continuous Character

Abstract Understanding how and why rates of character evolution vary across the Tree of Life is central to many evolutionary questions; for example, does the trophic apparatus (a set of continuous characters) evolve at a higher rate in fish lineages that dwell in reef versus nonreef habitats (a discrete character)? Existing approaches for inferring the relationship between a discrete character and rates of continuous-character evolution rely on comparing a null model (in which rates of continuous-character evolution are constant across lineages) to an alternative model (in which rates of continuous-character evolution depend on the state of the discrete character under consideration). However, these approaches are susceptible to a “straw-man” effect: the influence of the discrete character is inflated because the null model is extremely unrealistic. Here, we describe MuSSCRat, a Bayesian approach for inferring the impact of a discrete trait on rates of continuous-character evolution in the presence of alternative sources of rate variation (“background-rate variation”). We demonstrate by simulation that our method is able to reliably infer the degree of state-dependent rate variation, and show that ignoring background-rate variation leads to biased inferences regarding the degree of state-dependent rate variation in grunts (the fish group Haemulidae). [Bayesian phylogenetic comparative methods; continuous-character evolution; data augmentation; discrete-character evolution.]

scholarly journals A Bayesian Approach for Inferring the Impact of a Discrete Character on Rates of Continuous-Character Evolution in the Presence of Background-Rate Variation

2019 ◽  
Author(s):  
Michael R. May ◽  
Brian R. Moore
Keyword(s):  
Bayesian Approach ◽  
Null Model ◽  
Character Evolution ◽  
Rate Variation ◽  
Background Rate ◽  
Dependent Rate ◽  
State Dependent ◽  
Discrete Character ◽  
The Impact ◽  
Continuous Character

AbstractUnderstanding how and why rates of character evolution vary across the Tree of Life is central to many evolutionary questions; e.g., does the trophic apparatus (a set of continuous characters) evolve at a higher rate in fish lineages that dwell in reef versus non-reef habitats (a discrete character)? Existing approaches for inferring the relationship between a discrete character and rates of continuous-character evolution rely on comparing a null model (in which rates of continuous-character evolution are constant across lineages) to an alternative model (in which rates of continuous-character evolution depend on the state of the discrete character under consideration). However, these approaches are susceptible to a “straw-man” effect: the influence of the discrete character is inflated because the null model is extremely unrealistic. Here, we describe MuSSCRat, a Bayesian approach for inferring the impact of a discrete trait on rates of continuous-character evolution in the presence of alternative sources of rate variation (“background-rate variation”). We demonstrate by simulation that our method is able to reliably infer the degree of state-dependent rate variation, and show that ignoring background-rate variation leads to biased inferences regarding the degree of state-dependent rate variation in grunts (the fish group Haemulidae). [continuous-character evolution; discrete-character evolution; Bayesian phylogenetic comparative methods; data augmentation]

scholarly journals Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8744 ◽  
Author(s):  
Neil Brocklehurst ◽  
Gemma Louise Benevento
Keyword(s):  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Character Evolution ◽  
Rate Variation ◽  
Rates Of Evolution ◽  
Discrete Character ◽  
Osteological Characters

Accurate reconstructions of phylogeny are essential for studying the evolution of a clade, and morphological characters are necessarily used for the reconstruction of the relationships of fossil organisms. However, variation in their evolutionary modes (for example rate variation and character non-independence) not accounted for in analyses may be leading to unreliable phylogenies. A recent study suggested that phylogenetic analyses of mammals may be suffering from a dominance of dental characters, which were shown to have lower phylogenetic signal than osteological characters and produced phylogenies less congruent with molecularly-derived benchmarks. Here we build on this previous work by testing five additional morphological partitions for phylogenetic signal and examining what aspects of dental and other character evolution may be affecting this, by fitting models of discrete character evolution to phylogenies inferred and time calibrated using molecular data. Results indicate that the phylogenetic signal of discrete characters correlate most strongly with rates of evolution, with increased rates driving increased homoplasy. In a dataset covering all Mammalia, dental characters have higher rates of evolution than other partitions. They do not, however, fit a model of independent character evolution any worse than other regions. Primates and marsupials show different patterns to other mammal clades, with dental characters evolving at slower rates and being more heavily integrated (less independent). While the dominance of dental characters in analyses of mammals could be leading to inaccurate phylogenies, the issue is not unique to dental characters and the results are not consistent across datasets. Molecular benchmarks (being entirely independent of the character data) provide a framework for examining each dataset individually to assess the evolution of the characters used.

scholarly journals Molecular dating for phylogenies containing a mix of populations and species

2019 ◽  
Author(s):  
Beatriz Mello ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Bayesian Approach ◽  
Phylogenetic Trees ◽  
Molecular Dating ◽  
Rate Variation ◽  
Species Variation ◽  
Sequence Alignments ◽  
Clock Model ◽  
Divergence Time Estimates ◽  
The Impact ◽  
The Bayesian Approach

AbstractConcurrent molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics, and species delimitation studies. Multiple sequence alignments used in these investigations frequently consist of both intra- and inter-species samples (mixed samples). As a result, the phylogenetic trees contain inter-species, inter-population, and within population divergences. To date these sequence divergences, Bayesian relaxed clock methods are often employed, but they assume the same tree prior for both inter- and intra-species branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of using the same tree prior on the Bayesian divergence time estimates by analyzing computer-simulated datasets. We also examined the effect of the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with Skyline-coalescent tree priors generally produced excellent molecular dates, with some tree priors (e.g., Yule) performing the best when evolutionary rates were autocorrelated, and lineage sorting was incomplete. We compared the performance of the Bayesian approach with a non-Bayesian, the RelTime method, which does not require specification of a tree prior or selection of a clock model. We found that RelTime performed as well as the Bayesian approach, and when the clock model was mis-specified, RelTime performed slightly better. These results suggest that the computationally efficient RelTime approach is also suitable to analyze datasets containing both populations and species variation.

scholarly journals Detecting anomalous citation groups in journal networks

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sadamori Kojaku ◽  
Giacomo Livan ◽  
Naoki Masuda
Keyword(s):  
Null Model ◽  
Impact Factors ◽  
Academic Publishing ◽  
Scientific Communities ◽  
Citation Behavior ◽  
Journal Editors ◽  
Journal Citation Reports ◽  
Academic Climate ◽  
The Impact ◽  
Publication Standards

AbstractThe ever-increasing competitiveness in the academic publishing market incentivizes journal editors to pursue higher impact factors. This translates into journals becoming more selective, and, ultimately, into higher publication standards. However, the fixation on higher impact factors leads some journals to artificially boost impact factors through the coordinated effort of a “citation cartel” of journals. “Citation cartel” behavior has become increasingly common in recent years, with several instances being reported. Here, we propose an algorithm—named CIDRE—to detect anomalous groups of journals that exchange citations at excessively high rates when compared against a null model that accounts for scientific communities and journal size. CIDRE detects more than half of the journals suspended from Journal Citation Reports due to anomalous citation behavior in the year of suspension or in advance. Furthermore, CIDRE detects many new anomalous groups, where the impact factors of the member journals are lifted substantially higher by the citations from other member journals. We describe a number of such examples in detail and discuss the implications of our findings with regard to the current academic climate.

scholarly journals Synchronization in 5G networks: a hybrid Bayesian approach toward clock offset/skew estimation and its impact on localization

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Meysam Goodarzi ◽  
Darko Cvetkovski ◽  
Nebojsa Maletic ◽  
Jesús Gutiérrez ◽  
Eckhard Grass
Keyword(s):  
Bayesian Approach ◽  
Large Scale ◽  
Hybrid Approach ◽  
Position Estimation ◽  
5G Networks ◽  
Clock Skew ◽  
Depth Analysis ◽  
The Impact ◽  
Mean Square Errors ◽  
Clock Offset

AbstractClock synchronization has always been a major challenge when designing wireless networks. This work focuses on tackling the time synchronization problem in 5G networks by adopting a hybrid Bayesian approach for clock offset and skew estimation. Furthermore, we provide an in-depth analysis of the impact of the proposed approach on a synchronization-sensitive service, i.e., localization. Specifically, we expose the substantial benefit of belief propagation (BP) running on factor graphs (FGs) in achieving precise network-wide synchronization. Moreover, we take advantage of Bayesian recursive filtering (BRF) to mitigate the time-stamping error in pairwise synchronization. Finally, we reveal the merit of hybrid synchronization by dividing a large-scale network into local synchronization domains and applying the most suitable synchronization algorithm (BP- or BRF-based) on each domain. The performance of the hybrid approach is then evaluated in terms of the root mean square errors (RMSEs) of the clock offset, clock skew, and the position estimation. According to the simulations, in spite of the simplifications in the hybrid approach, RMSEs of clock offset, clock skew, and position estimation remain below 10 ns, 1 ppm, and 1.5 m, respectively.

PD-0776 A Bayesian approach to evaluate the impact of change in IGRT protocol using real world data

2021 ◽  
Vol 161 ◽  
pp. S608
Author(s):  
I. Fornacon-Wood ◽  
H. Mistry ◽  
C. Johnson-Hart ◽  
J.P.B. O’Connor ◽  
C. Faivre-Finn ◽  
...  
Keyword(s):  
Bayesian Approach ◽  
Real World ◽  
Real World Data ◽  
World Data ◽  
The Impact

scholarly journals Cast Iron Cooling Rate Variation Using Cooling Channels: A Numerical Approach

2021 ◽  
pp. 29-35
Author(s):  
Olumide Adewole Towoju
Keyword(s):  
Mechanical Properties ◽  
Cast Iron ◽  
Cooling Rate ◽  
Flow Rate ◽  
Numerical Approach ◽  
Cooling Curve ◽  
Rate Variation ◽  
Cooling Fluid ◽  
Cooling Channels ◽  
The Impact

The cooling rate of molten cast iron can make or mar it. The cooling rate plays a significant role in the resulting mechanical properties of cast iron. It determines the grain growth and size. The mechanical properties of cast iron variation along its length are achieved either with the use of different mold materials or by sectioning to ensure varied cooling rates. Mechanical properties can, however, also be varied along its length without any of these adopted methods by the incorporation of cooling channels in the mould. This study seeks to expand the frontier of this concept with the use of different cooling fluids and fluid flow rate, and numerically investigate the impact on the cooling rate of gray cast iron (class 40). The cooling curve for the cast iron was impacted by the use of different cooling fluids with the attainment of the desired mechanical properties with the selection of an appropriate cooling fluid. Also, the flow rate of the cooling fluid has an impact on the cast iron cooling rate.

scholarly journals The Basics of Bayesian Approach to Quantitative Analysis (at the Example of Euroscepticism)

2021 ◽  
pp. 301-321
Author(s):  
Aleksey Domanov
Keyword(s):  
Bayesian Approach ◽  
Quantitative Methods ◽  
Explanatory Power ◽  
Life Quality ◽  
Likelihood Estimation ◽  
Event Analysis ◽  
Research Areas ◽  
True Value ◽  
Predictive Algorithms ◽  
The Impact

This article attempts to identify the main assumptions, prerequisites and techniques of the methods developed by some modern statisticians on the basis of T. Bayes' theorem for the purposes of social variables interactions assessment. The author underlined several advantages of the given approach as compared to more traditional quantitative methods and highlighted key research areas subject to evaluation by Bayesian estimates. First of all, this approach is compatible with game and decision theory, event analysis, hidden Markov chains, prediction using neural networks and other predictive algorithms of artificial intelligence. The Bayesian approach differs significantly from traditional statistical methods (first of all, it is focused on finding the most probable, rather than the only true value of the feature coupling coefficient), hence a graphical interpretation was provided for such basic concepts and techniques as probabilistic inference, maximum likelihood estimation and Bayesian confidence network. The described tools were used to test the hypothesis about the impact of life quality decrease on rise in Euroscepticism of EU citizens. ANOVA and correlation analysis of 27 thousand people’s responses to Eurobarometer questions addressed in November-December 2019 attributed strong likelihood to this assumption. Moreover, Bayesian approach allowed for a probabilistic conclusion that this hypothesis is more plausible than the link between Euroscepticism and respondents’ current financial situation (explanatory power of comparison to the past is relatively greater).

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