II.—A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F. R. S

Yule, George

doi:10.1098/rstb.1925.0002

Cited by 1,439 publications

(507 citation statements)

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“…tRNAs were predicted using tRNAscan-SE 40 . All predicted proteins were functionally annotated using SignalP 41 for signal sequences, TMHMM 42 for transmembrane domains, interProScan 43 59 and a Yule tree prior 60 .…”

Section: Methodsmentioning

confidence: 99%

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Möck

Otillar

Strauss

et al. 2017

Nature

322

303

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The Southern Ocean houses a diverse and productive community of organisms 1,2 . Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice 3-7 . How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus 8,9 , based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation.

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Section: Methodsmentioning

confidence: 99%

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Möck

Otillar

Strauss

et al. 2017

Nature

322

303

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“…In the following, time 0 is today and t or the origin of the tree, so time is increasing going into the past. Special cases of the birth-death process are the Yule model (Yule, 1924) where µ = 0 and the critical branching process (Aldous and Popovic, 2005;Popovic, 2004) where µ = λ. When looking at phylogenies, we have a given number, say n, of extant taxa.…”

Section: Introductionmentioning

confidence: 99%

The conditioned reconstructed process

Gernhard

2008

Journal of Theoretical Biology

895

647

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We investigate a neutral model for speciation and extinction, the constant rate birth-death process. The process is conditioned to have n extant species today, we look at the tree distribution of the reconstructed trees-i.e. the trees without the extinct species. Whereas the tree shape distribution is well-known and actually the same as under the pure birth process, no analytic results for the speciation times were known. We provide the distribution for the speciation times and calculate the expectations analytically. This characterizes the reconstructed trees completely. We will show how the results can be used to date phylogenies.

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“…The first to show that using a stochastic process to model the evolution of a population may lead to a distribution with a power-law tail was Udny Yule [746]. Appropriately, this work was done in the context of providing a mathematical model for the theory of evolution.…”

Section: Preferential Attachmentmentioning

confidence: 99%

Workload Modeling for Computer Systems Performance Evaluation

Feitelson

2015

191

131

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Reliable performance evaluations require the use of representative workloads. This is no easy task since modern computer systems and their workloads are complex, with many interrelated attributes and complicated structures. Experts often use sophisticated mathematics to analyze and describe workload models, making these models difficult for practitioners to grasp. This book aims to close this gap by emphasizing the intuition and the reasoning behind the definitions and derivations related to the workload models. It provides numerous examples from real production systems, with hundreds of graphs. Using this book, readers will be able to analyze collected workload data and clean it if necessary, derive statistical models that include skewed marginal distributions and correlations, and consider the need for generative models and feedback from the system. The descriptive statistics techniques covered are also useful for other domains.

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II.—A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F. R. S

Cited by 1,439 publications

References 0 publications

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

The conditioned reconstructed process

Workload Modeling for Computer Systems Performance Evaluation

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