scholarly journals Exploring DSL Evolutionary Patterns in Practice - A Study of DSL Evolution in a Large-scale Industrial DSL Repository

2018 ◽  
Author(s):  
Josh G. M. Mengerink ◽  
Bram van der Sanden ◽  
Bram C. M. Cappers ◽  
Alexander Serebrenik ◽  
Ramon R. H. Schiffelers ◽  
...  
Keyword(s):  
Large Scale ◽  
Evolutionary Patterns

The biology of mass extinction: a palaeontological view

1989 ◽  
Vol 325 (1228) ◽  
pp. 357-368 ◽  
Keyword(s):  
Mass Extinction ◽  
Large Scale ◽  
Individual Species ◽  
Ecological Groups ◽  
Mass Extinctions ◽  
Geological Time ◽  
Evolutionary Patterns ◽  
Data Set ◽  
High Species Richness ◽  
Extinction Events

Extinctions are not biologically random: certain taxa or functional/ecological groups are more extinction-prone than others. Analysis of molluscan survivorship patterns for the end-Cretaceous mass extinctions suggests that some traits that tend to confer extinction resistance during times of normal (‘background’) levels of extinction are ineffectual during mass extinction. For genera, high species-richness and possession of widespread individual species imparted extinction-resistance during background times but not during the mass extinction, when overall distribution of the genus was an important factor. Reanalysis of Hoffman’s (1986) data ( Neues Jb. Geol. Palaont. Abh. 172, 219) on European bivalves, and preliminary analysis of a new northern European data set, reveals a similar change in survivorship rules, as do data scattered among other taxa and extinction events. Thus taxa and adaptations can be lost not because they were poorly adapted by the standards of the background processes that constitute the bulk of geological time, but because they lacked - or were not linked to - the organismic, species-level or clade-level traits favoured under mass-extinction conditions. Mass extinctions can break the hegemony of species-rich, well-adapted clades and thereby permit radiation of taxa that had previously been minor faunal elements; no net increase in the adaptation of the biota need ensue. Although some large-scale evolutionary trends transcend mass extinctions, post-extinction evolutionary pathways are often channelled in directions not predictable from evolutionary patterns during background times.

scholarly journals Large-Scale Evolutionary Patterns of Protein Domain Distributions in Eukaryotes

2017 ◽  
Author(s):  
Arli A. Parikesit ◽  
Peter F. Stadler ◽  
Sonja J. Prohaska
Keyword(s):  
Large Scale ◽  
Gene Prediction ◽  
Protein Domains ◽  
Protein Domain ◽  
Medical Sciences ◽  
Evolutionary Patterns ◽  
Important Indicator ◽  
Domain Annotation ◽  
Species Specific ◽  
High Level

AbstractThe genomic inventory of protein domains is an important indicator of an organism’s regulatory and metabolic capabilities. Existing gene annotations, however, can be plagued by substantial ascertainment biases that make it difficult to obtain and compare quantitative domain data. We find that quantitative trends across the Eukarya can be investigated based on a combination of gene prediction and standard domain annotation pipelines. Species-specific training is required, however, to account for the genomic peculiarities in many lineages. In contrast to earlier studies we find wide-spread statistically significant avoidance of protein domains associated with distinct functional high-level gene-ontology terms.1998 ACM Subject Classification J.3 Life and Medical Sciences

scholarly journals MG-DVD: A Real-time Framework for Malware Variant Detection Based on Dynamic Heterogeneous Graph Learning

2021 ◽  
Author(s):  
Chen Liu ◽  
Bo Li ◽  
Jun Zhao ◽  
Ming Su ◽  
Xu-Dong Liu
Keyword(s):  
Real Time ◽  
Real World ◽  
Large Scale ◽  
State Of The Art ◽  
Evolutionary Patterns ◽  
Graph Learning ◽  
Fine Grained ◽  
Variant Detection ◽  
Effectiveness And Efficiency ◽  
The Cost

Detecting the newly emerging malware variants in real time is crucial for mitigating cyber risks and proactively blocking intrusions. In this paper, we propose MG-DVD, a novel detection framework based on dynamic heterogeneous graph learning, to detect malware variants in real time. Particularly, MG-DVD first models the fine-grained execution event streams of malware variants into dynamic heterogeneous graphs and investigates real-world meta-graphs between malware objects, which can effectively characterize more discriminative malicious evolutionary patterns between malware and their variants. Then, MG-DVD presents two dynamic walk-based heterogeneous graph learning methods to learn more comprehensive representations of malware variants, which significantly reduces the cost of the entire graph retraining. As a result, MG-DVD is equipped with the ability to detect malware variants in real time, and it presents better interpretability by introducing meaningful meta-graphs. Comprehensive experiments on large-scale samples prove that our proposed MG-DVD outperforms state-of-the-art methods in detecting malware variants in terms of effectiveness and efficiency.

Phylogenetic corrections for morphological disparity analysis: new methodology and case studies

Paleobiology ◽  
2011 ◽  
Vol 37 (1) ◽  
pp. 1-22 ◽  
Author(s):  
Stephen L. Brusatte ◽  
Shaena Montanari ◽  
Hong-yu Yi ◽  
Mark A. Norell
Keyword(s):  
Large Scale ◽  
Evolutionary Rate ◽  
Taxonomic Diversity ◽  
Data Sets ◽  
Time Intervals ◽  
Evolutionary Patterns ◽  
Morphological Disparity ◽  
Discrete Character ◽  
Fossil Records ◽  
General Method

Taxonomic diversity and morphological disparity are different measures of biodiversity that together can describe large-scale evolutionary patterns. Diversity measures are often corrected by extending lineages back in time or adding additional taxa necessitated by a phylogeny, but disparity analyses focus on observed taxa only. This is problematic because some morphologies required by phylogeny are not included, some of which may help fill poorly sampled time bins. Moreover the taxic nature of disparity analyses makes it difficult to compare disparity measures with phylogenetically corrected diversity or morphological evolutionary rate curves. We present a general method for using phylogeny to correct measures of disparity, by including reconstructed ancestors in the disparity analysis. We apply this method to discrete character data sets focusing on Triassic archosaurs, Cenozoic carnivoramorph mammals, and Cretaceous-Cenozoic euarchontogliran mammals. Phylogenetic corrections do not simply mirror the taxic disparity patterns, but affect the three analyses in heterogeneous ways. Adding reconstructed ancestors can inflate morphospace, and the amount and direction of expansion differs depending on the taxonomic group in question. In some cases phylogenetic corrections give a temporal disparity curve indistinguishable from the taxic trend, but in other cases disparity is elevated in earlier time intervals relative to later bins, due to the extension of unsampled morphologies further back in time. The phylogenetic disparity curve for archosaurs differs little from the taxic curve, supporting a previously documented pattern of decoupled disparity and rates of morphological change in dinosaurs and their early contemporaries. Although phylogenetic corrections should not be used blindly, they are helpful when studying clades with major unsampled gaps in their fossil records.

scholarly journals VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data

2005 ◽  
Vol 21 (11) ◽  
pp. 2791-2793 ◽  
Author(s):  
A. J. Vilella ◽  
A. Blanco-Garcia ◽  
S. Hutter ◽  
J. Rozas
Keyword(s):  
Dna Sequence ◽  
Large Scale ◽  
Sequence Polymorphism ◽  
Evolutionary Patterns ◽  
Dna Sequence Polymorphism ◽  
Polymorphism Data

scholarly journals The late blooming amphipods: global change promoted post-Jurassic ecological radiation despite Palaeozoic origin

2019 ◽  
Author(s):  
Denis Copilaş-Ciocianu ◽  
Špela Borko ◽  
Cene Fišer
Keyword(s):  
Deep Sea ◽  
Large Scale ◽  
Global Changes ◽  
Ecological Divergence ◽  
Evolutionary Patterns ◽  
Late Mesozoic ◽  
Ecological Diversification ◽  
Late Palaeozoic ◽  
Ecological Radiation ◽  
Marine Littoral

AbstractThe ecological radiation of amphipods is striking among crustaceans. Despite high diversity, global distribution and key roles in all aquatic environments, little is known about their ecological transitions, evolutionary timescale and phylogenetic relationships. It has been proposed that the amphipod ecological diversification began in the Late Palaeozoic. By contrast, due to their affinity for cold/oxygenated water and absence of pre-Cenozoic fossils, we hypothesized that the ecological divergence of amphipods arose throughout the cool Late Mesozoic/Cenozoic. We tested our hypothesis by inferring a large-scale, time-calibrated, multilocus phylogeny, and reconstructed evolutionary patterns for major ecological traits. Although our results reveal a Late Palaeozoic amphipod origin, diversification and ecological divergence ensued only in the Late Mesozoic, overcoming a protracted stasis in marine littoral habitats. Multiple independent post-Jurassic radiations took place in deep-sea, freshwater, terrestrial, pelagic and symbiotic environments, usually postdating deep-sea faunal extinctions, and corresponding with significant climatic cooling, tectonic reconfiguration, continental flooding, and increased oceanic oxygenation. We conclude that the profound Late Mesozoic global changes triggered a tipping point in amphipod evolution by unlocking ecological opportunities that promoted radiation into many new niches. Our study also provides a solid, time-calibrated, evolutionary framework to accelerate research on this overlooked, yet globally important taxon.

Visualizing the Evolution of Programming Languages

Leonardo ◽  
2017 ◽  
Vol 50 (5) ◽  
pp. 505-505
Author(s):  
Sergi Valverde
Keyword(s):  
Programming Languages ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Quantitative Methods ◽  
Technological Evolution ◽  
Network Approach ◽  
Evolutionary Patterns ◽  
Cultural Evolutionary ◽  
Simple Network ◽  
Scale Evolution

The study of cultural evolutionary patterns, particularly when dealing with artifacts, is constrained by a lack of powerful quantitative methods. In this work, the project team shows that a simple network approach can reconstruct phylogenetic trees from existing databases of recorded artifact influences. They created novel network tools to visualize the large-scale evolution of programming languages. The simple idea of trees of influence can be extended to many other fields beyond the study of programming languages, offering a new theoretical framework to rigorously quantify cultural and technological evolution.

scholarly journals Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2402 ◽  
Author(s):  
Kyle Dexter ◽  
Jérôme Chave
Keyword(s):  
Species Richness ◽  
Large Scale ◽  
Amazon Basin ◽  
Phylogenetic Signal ◽  
Negative Relationship ◽  
Range Size ◽  
Evolutionary Patterns ◽  
Intrinsic Factors ◽  
Significant Negative Relationship ◽  
Amazonian Trees

Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. The drivers of this variation are not well understood. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to contribute to explaining the variation. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics; closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species. Our results suggest that phylogenetically correlated intrinsic factors, namely traits of the genera themselves, shape among lineage variation in range size, abundance and species richness. We postulate that tree stature may be one particularly relevant trait. However, other traits may also be relevant, and our study reinforces the need for ambitious compilations of trait data for Amazonian trees. In the meantime, our study shows how large-scale phylogenies can help to elucidate, and contribute to explaining, macroecological and macroevolutionary patterns in hyperdiverse, yet poorly understood regions like the Amazon Basin.

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