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Beneficial and deleterious mutations cause the fitness of lineages to vary across a phylogeny and thereby shape its branching structure. While standard phylogenetic models do not allow mutations to feedback and shape trees, birth-death models can account for this feedback by letting the fitness of lineages depend on their type. To date, these multi-type birth-death models have only been applied to cases where a lineage's fitness is determined by a single character state. We extend these models to track sequence evolution at multiple sites. This approach remains computationally tractable by tracking the genotype and fitness of lineages probabilistically in an approximate manner. Although approximate, we show that we can accurately estimate the fitness of lineages and site-specific mutational fitness effects from phylogenies. We apply this approach to estimate the population-level fitness effects of mutations in Ebola and influenza virus, and compare our estimates with in vitro fitness measurements for these mutations.
This article was published in the following journal.
Adaptive mutations play an important role in molecular evolution. However, the frequency and nature of these mutations at the intra-molecular level is poorly understood. To address this, we analysed t...
Estimation of adaptive evolution rates at the molecular level is important in evolutionary genomics. However, knowledge of adaptive evolutionary patterns in Mollusca is very scarce, especially for oys...
I distinguish two roles for a fitness concept in the context of explaining cumulative adaptive evolution: fitness as a predictor of gene frequency change, and fitness as a criterion for phenotypic imp...
Transition bias, an overabundance of transitions relative to transversions, has been widely reported among studies of the rates and spectra of spontaneous mutations. However, demonstrating the role of...
When prescribing a prosthetic foot, clinicians face a dizzying array of choices as more than 200 different prosthetic feet are available. While these conventional prosthetic feet primarily...
The objective of this Bayesian Adaptive trial is to compare a control group versus a comprehensive ulcer healing protocol. The latter involves a combination of compressive therapy, miokine...
This study aims to examine the evolution and determinants of physical fitness after stroke.
This study proposes to use a new instrument (AO-OCT/AF: adaptive optics - optical coherence tomography/autofluorescence) combined with a data processing method to image the retinal pigment...
Background: Depending on nature and needs, physical fitness can be divided into healthy fitness and physical fitness (also known as competitive fitness). Healthy fitness includes cardio-re...
Evolution at the molecular level of DNA sequences and proteins. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
The relative amount by which the average fitness of a POPULATION is lowered, due to the presence of GENES that decrease survival, compared to the GENOTYPE with maximum or optimal fitness. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
The techniques used to produce molecules exhibiting properties that conform to the demands of the experimenter. These techniques combine methods of generating structural changes with methods of selection. They are also used to examine proposed mechanisms of evolution under in vitro selection conditions.
The interdisciplinary science that studies evolutionary biology, including the origin and evolution of the major elements required for life, their processing in the interstellar medium and in protostellar systems. This field also includes the study of chemical evolution and the subsequent interactions between evolving biota and planetary evolution as well as the field of biology that deals with the study of extraterrestrial life.
The reaction of two molecular entities via oxidation usually catalyzed by a transition metal compound and involving dioxygen as the oxidant.
Tropical Medicine is the study of diseases more commonly found in tropical regions than elsewhere. Examples of these diseases are malaria, yellow fever, Chagas disease, Dengue, Helminths, African trypanosomiasis, Leishmaniasis, Leprosy, Lymphatic filaria...
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