scholarly journals Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

Author(s):  
Joseph F. Walker ◽  
Xing-Xing Shen ◽  
Antonis Rokas ◽  
Stephen A. Smith ◽  
Edwige Moyroud

AbstractThe genomic data revolution has enabled biologists to develop innovative ways to infer key episodes in the history of life. Whether genome-scale data will eventually resolve all branches of the Tree of Life remains uncertain. However, through novel means of interrogating data, some explanations for why evolutionary relationships remain recalcitrant are emerging. Here, we provide four biological and analytical factors that explain why certain genes may exhibit “outlier” behavior, namely, rate of molecular evolution, alignment length, misidentified orthology, and errors in modeling. Using empirical and simulated data we show how excluding genes based on their likelihood or inferring processes from the topology they support in a supermatrix can mislead biological inference of conflict. We next show alignment length accounts for the high influence of two genes reported in empirical datasets. Finally, we also reiterate the impact misidentified orthology and short alignments have on likelihoods in large scale phylogenetics. We suggest that researchers should systematically investigate and describe the source of influential genes, as opposed to discarding them as outliers. Disentangling whether analytical or biological factors are the source of outliers will help uncover new patterns and processes that are shaping the Tree of Life.

Author(s):  
Krzysztof Jurczuk ◽  
Marcin Czajkowski ◽  
Marek Kretowski

AbstractThis paper concerns the evolutionary induction of decision trees (DT) for large-scale data. Such a global approach is one of the alternatives to the top-down inducers. It searches for the tree structure and tests simultaneously and thus gives improvements in the prediction and size of resulting classifiers in many situations. However, it is the population-based and iterative approach that can be too computationally demanding to apply for big data mining directly. The paper demonstrates that this barrier can be overcome by smart distributed/parallel processing. Moreover, we ask the question whether the global approach can truly compete with the greedy systems for large-scale data. For this purpose, we propose a novel multi-GPU approach. It incorporates the knowledge of global DT induction and evolutionary algorithm parallelization together with efficient utilization of memory and computing GPU’s resources. The searches for the tree structure and tests are performed simultaneously on a CPU, while the fitness calculations are delegated to GPUs. Data-parallel decomposition strategy and CUDA framework are applied. Experimental validation is performed on both artificial and real-life datasets. In both cases, the obtained acceleration is very satisfactory. The solution is able to process even billions of instances in a few hours on a single workstation equipped with 4 GPUs. The impact of data characteristics (size and dimension) on convergence and speedup of the evolutionary search is also shown. When the number of GPUs grows, nearly linear scalability is observed what suggests that data size boundaries for evolutionary DT mining are fading.


Author(s):  
Luigi Rizzi

This chapter illustrates the technical notion of ‘explanatory adequacy’ in the context of the other forms of empirical adequacy envisaged in the history of generative grammar: an analysis of a linguistic phenomenon is said to meet ‘explanatory adequacy’ when it comes with a reasonable account of how the phenomenon is acquired by the language learner. It discusses the relevance of arguments from the poverty of the stimulus, which bear on the complexity of the task that every language learner successfully accomplishes, and therefore define critical cases for evaluating the explanatory adequacy of a linguistic analysis. After illustrating the impact that parametric models had on the possibility of achieving explanatory adequacy on a large scale, the chapter addresses the role that explanatory adequacy plays in the context of the Minimalist Program, and the interplay that the concept has with the further explanation ‘beyond explanatory adequacy’ that minimalist analysis seeks.


Author(s):  
D.V. Budianskyi

The characteristic features of I. Kavaleridze’s drama is considered in the article. It is noted that there are signs of the artist’s individuality, attraction to expressionist forms, artistic techniques characteristic for the art of sculpture: symbolism, monumentality, hyperbole. I. Kavaleridze was well versed in the drama laws, understood the specifics of the stage events construction, had a large arsenal of literary means, thanks to which the characters’ monologues and dialogues were extremely expressive and colorful. In his work, he implemented original solutions that were ahead of time. Therefore, many of the artist’s ideas and achievements received due recognition only after his death. I. Kavaleridze’s creative heritage covers a wide range of both purely artistic and general philosophical problems. Among them the formation of the era of modernism and its features in the Ukrainian art of the early XX century, the impact of revolutionary ideas on the work of the 1920s, the role of spiritual leaders of the Ukrainian people T. Shevchenko and G. Skovoroda in the formation of national consciousness, political and ideological pressure on figurative art language and the formation of a socialist-realist canon, etc. The analysis of the productions of I. Kavalerizde’s plays “The First Furrow” and “Gregory and Paraskeva” on the stage of the Mykhailo Shchepkin Sumy Theater of Drama and Musical Comedy in 1970-1972. The article notes that these plays were staged in Sumy for the first time in the history of Ukrainian theater. The premiere of “The First Furrow” (the play was called “Old Men”) took place on March 19, 1970. The figure of the national genius Hryhoriy Skov oroda was als o embodied for the first time on t he stage in Sumy in th e play “Hryhoriy and Paraskeva”. It premiered on October 21, 1972. I. Rybchynsky, Honored Artist of the USSR, performed the production. Creating generalized historical outlines of people’s life, features of life at that time, depicting psychological portraits of people in various, sometimes-dramatic collisions, in the productions of I. Kavaleridze’s plays on the Sumy stage the emphasis was on universal values such as virtue, love. The main character was the Ukrainian people, who nurtured such large-scale historical figures, gave them strength and wisdom for great achievements. Based on publications in periodicals of that time, memoirs of Ukrainian directors, the peculiarities of the director’s interpretation, stenographic and musical design of these plays on the Sumy stage are considered. Considerable attention is paid to the analysis of acting works in I. Kavaleridze’s plays. In particular, the peculiarities of the actor’s embodiment of the image of the national genius Hryhoriy Skovoroda on the stage are presented. It is noted that I. Kavaleridze’s plays, created in a difficult political, social and ideological context, are rightly considered to be highly artistic works of Ukrainian drama. Their staging was carried out on various theatrical stages, including Mykhailo Shchepkin Sumy Theater of Drama and Musical Comedy is an important page of national theatrical art.


Author(s):  
Nenad Jukic ◽  
Miguel Velasco

Defining data warehouse requirements is widely recognized as one of the most important steps in the larger data warehouse system development process. This paper examines the potential risks and pitfalls within the data warehouse requirement collection and definition process. A real scenario of a large-scale data warehouse implementation is given, and details of this project, which ultimately failed due to inadequate requirement collection and definition process, are described. The presented case underscores and illustrates the impact of the requirement collection and definition process on the data warehouse implementation, while the case is analyzed within the context of the existing approaches, methodologies, and best practices for prevention and avoidance of typical data warehouse requirement errors and oversights.


2010 ◽  
Vol 1 (3) ◽  
pp. 66-76
Author(s):  
Nenad Jukic ◽  
Miguel Velasco

Defining data warehouse requirements is widely recognized as one of the most important steps in the larger data warehouse system development process. This paper examines the potential risks and pitfalls within the data warehouse requirement collection and definition process. A real scenario of a large-scale data warehouse implementation is given, and details of this project, which ultimately failed due to inadequate requirement collection and definition process, are described. The presented case underscores and illustrates the impact of the requirement collection and definition process on the data warehouse implementation, while the case is analyzed within the context of the existing approaches, methodologies, and best practices for prevention and avoidance of typical data warehouse requirement errors and oversights.


2019 ◽  
Vol 5 (4) ◽  
pp. 695-702 ◽  
Author(s):  
Julien Morency-Laflamme ◽  
Theodore McLauchlin

Abstract Does ethnic stacking in the armed forces help prevent military defection? Recent research, particularly in Africa and the Middle East, suggests so; by favoring in-groups, regimes can keep in-group soldiers loyal. In-group loyalty comes at the cost of antagonizing members of out-groups, but many regimes gladly run that risk. In this research note, we provide the first large-scale evidence on the impact of ethnic stacking on the incidence of military defection during uprisings from below, using data on fifty-seven popular uprisings in Africa since formal independence. We find clear evidence for the downside: ethnic stacking is associated with more frequent defection if out-group members are still dominant in the armed forces. We find more limited support for the hypothesized payoff. Ethnic stacking may reduce the risk of defection, but only in regimes without a recent history of coup attempts. Future research should therefore trace the solidification of ethnic stacking over time.


Author(s):  
Anne H Klein ◽  
Kaylene R Ballard ◽  
Kenneth B Storey ◽  
Cherie A Motti ◽  
Min Zhao ◽  
...  

Abstract Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics (‘gastropodomics’) research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.


IMA Fungus ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Claudio G. Ametrano ◽  
Felix Grewe ◽  
Pedro W. Crous ◽  
Stephen B. Goodwin ◽  
Chen Liang ◽  
...  

Abstract Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.


2013 ◽  
Vol 40 (1) ◽  
pp. 115-143 ◽  
Author(s):  
Nikolai M. Dronin ◽  
Andrei P. Kirilenko

Agriculture in Russia has always had to contend with unfavorable climate. At the same time, large-scale socio-economic experiments have also strained the country’s food production potential throughout the 20th century. The relative role of climate and state agricultural policies in affecting production of cereals was studied for the period of 1958–2010. The study used statistical yield modeling to explain the variations in observed yields with slowly changing progress in technology and management and weather variability. The correlation between the actual and weather-explained yields is moderate to high: measured at the level of the entire country, Pearson’s r is 0.74 and Spearman’s rho is 0.68. Further, we suggest that the residual yield variability can be explained partially with the influence of large-scale changes in agricultural policies at the state level. Between these policies, we consider the following key periods in the history of Russian agriculture: “Virgin Lands” campaign (end of 1950s), Kosygin-Liberman initiatives (late 1960s), Brezhnev’s investment programmes in response of stagnation of agriculture (late 1970s – early 1980s), Gorbachev’s “Perestrojka” (1985–1991), and land privatization and price liberalization (1990s).


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