Inferring ancestral sequences in taxon-rich phylogenies.

Abstract:

:Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, it is also useful to consider a dual type of statistical consistency where we increase the number of species, rather than characters. This raises some basic questions: what can we learn about the evolutionary process as we increase the number of species? In particular, does having more species allow us to infer the ancestral state of characters accurately? This question is particularly important when sequence evolution varies in a complex way from character to character, as methods applicable for i.i.d. models may no longer be valid. In this paper, we assemble a collection of results to analyse various approaches for inferring ancestral information with increasing accuracy as the number of taxa increases.

journal_name

Math Biosci

journal_title

Mathematical biosciences

authors

Gascuel O,Steel M

doi

10.1016/j.mbs.2010.07.002

subject

Has Abstract

pub_date

2010-10-01 00:00:00

pages

125-35

issue

2

eissn

0025-5564

issn

1879-3134

pii

S0025-5564(10)00110-0

journal_volume

227

pub_type

杂志文章
  • Four-state models and regulation of contraction of smooth muscle. I. Physical considerations, stability, and solutions.

    abstract::Cyclic four-state models are frequently used in biology to represent a variety of molecular behaviors. A common experimental strategy to test such models is to follow the behavior of the real system after some of the rate constants are changed in a stepwise manner. We analyze the mathematical behavior of a simple exam...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/0025-5564(92)90086-c

    authors: Lazalde CA,Barr L

    更新日期:1992-11-01 00:00:00

  • Effective rate models for the analysis of transport-dependent biosensor data.

    abstract::Optical biosensors, including the BIACORE, provide an increasingly popular method for determining reaction rates of biomolecules. In a flow chamber, with one reactant immobilized on a chip on the sensor surface, a solution containing the other reactant (the analyte) flows through the chamber. The time course of bindin...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/s0025-5564(99)00023-1

    authors: Mason T,Pineda AR,Wofsy C,Goldstein B

    更新日期:1999-07-01 00:00:00

  • Size distributions of misrejoining DNA fragments in irradiated cells.

    abstract::When ionizing radiation strikes a cell it induces DNA double strand breaks (DSBs). Subsequently, some of the DSBs misrejoin and thus cause alterations in the size distribution of the DNA fragments. We derive a system of non-linear integro-differential equations describing the misrejoining interactions of five classes ...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章,评审

    doi:10.1016/s0025-5564(98)00006-6

    authors: Radivoyevitch T,Hoel DG,Hahnfeldt P,Sachs RK

    更新日期:1998-05-01 00:00:00

  • Hopf bifurcation in three-species food chain models with group defense.

    abstract::Three-species food-chain models, in which the prey population exhibits group defense, are considered. Using the carrying capacity of the environment as the bifurcation parameter, it is shown that the model without delay undergoes a sequence of Hopf bifurcations. In the model with delay it is shown that using a delay a...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/0025-5564(92)90079-c

    authors: Freedman HI,Ruan S

    更新日期:1992-09-01 00:00:00

  • Influence of tissue metabolism and capillary oxygen supply on arteriolar oxygen transport: a computational model.

    abstract::We present a theoretical model for steady-state radial and longitudinal oxygen transport in arterioles containing flowing blood (plasma and red blood cells) and surrounded by living tissue. This model combines a detailed description of convective and diffusive oxygen transport inside the arteriole with a novel boundar...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2011.03.010

    authors: Moschandreou TE,Ellis CG,Goldman D

    更新日期:2011-07-01 00:00:00

  • An allelopathy based model for the Listeria overgrowth phenomenon.

    abstract::In a standard procedure of food safety testing, the presence of the pathogenic bacterium Listeria monocytogenes can be masked by non-pathogenic Listeria. This phenomenon of Listeria overgrowth is not well understood. We present a mathematical model for the growth of a mixed population of L. innocua and L. monocytogene...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2013.10.008

    authors: Fgaier H,Kalmokoff M,Ells T,Eberl HJ

    更新日期:2014-01-01 00:00:00

  • A class of phylogenetic networks reconstructable from ancestral profiles.

    abstract::Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set X of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate processes (for example, hybrid evolution, endosymbiosis, and lateral gene transfer). A...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2019.04.009

    authors: Erdős PL,Semple C,Steel M

    更新日期:2019-07-01 00:00:00

  • An algebraic analysis of the two state Markov model on tripod trees.

    abstract::Methods of phylogenetic inference use more and more complex models to generate trees from data. However, even simple models and their implications are not fully understood. Here, we investigate the two-state Markov model on a tripod tree, inferring conditions under which a given set of observations gives rise to such ...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2012.03.001

    authors: Klaere S,Liebscher V

    更新日期:2012-05-01 00:00:00

  • Material modeling of biofilm mechanical properties.

    abstract::A biofilm material model and a procedure for numerical integration are developed in this article. They enable calculation of a composite Young's modulus that varies in the biofilm and evolves with deformation. The biofilm-material model makes it possible to introduce a modeling example, produced by the Unified Multi-C...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2014.02.007

    authors: Laspidou CS,Spyrou LA,Aravas N,Rittmann BE

    更新日期:2014-05-01 00:00:00

  • Permanence of sparse catalytic networks.

    abstract::Some global dynamical properties of catalytic networks, in particular permanence, are closely related with a directed graph representing the differential equation. It can be shown that for every directed graph with a Hamiltonian circuit there is a choice of rate constants such that the system is permanent. On the othe...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/0025-5564(95)00033-x

    authors: Stadler PF,Schuster P

    更新日期:1996-01-15 00:00:00

  • Optimal control of receptor reinsertion in the low density lipoprotein endocytic cycle.

    abstract::On the basis of this study, it is concluded that within physiological limits the minimum value for the mean capture time of LDL receptors by coated pits must be induced fundamentally by an optimal characterization of their insertion rate function. The corresponding steady-state surface aggregation patterns for the unb...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/s0025-5564(99)00043-7

    authors: Echavarría-Heras H

    更新日期:1999-11-01 00:00:00

  • Model parameter uncertainties in a dual-species biofilm competition model affect ecological output parameters much stronger than morphological ones.

    abstract::Bacterial biofilms are complex microbial depositions on immersed interfaces that form wherever the environmental conditions sustain microbial growth. Despite their name, biofilms can develop in highly irregular structures. Recently several mathematical concepts have been introduced to model these spatially structured ...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2011.05.006

    authors: Muhammad N,Eberl HJ

    更新日期:2011-09-01 00:00:00

  • Spectra-based estimates of certain time-domain parameters of a bivariate stationary-point process.

    abstract::We consider estimates of certain time-domain parameters of a bivariate stationary-point process based on modified periodogram statistics. These estimates are shown to be asymptotically normal under regularity conditions. In the computations of the estimates, the advantage of using the FFT algorithm is demonstrated. Th...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/0025-5564(91)90061-m

    authors: Rigas AG

    更新日期:1991-05-01 00:00:00

  • Growth of necrotic tumors in the presence and absence of inhibitors.

    abstract::A mathematical model is presented for the growth of a multicellular spheroid that comprises a central core of necrotic cells surrounded by an outer annulus of proliferating cells. The model distinguishes two mechanisms for cell loss: apoptosis and necrosis. Cell loss due to apoptosis is defined to be programmed cell d...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/0025-5564(96)00023-5

    authors: Byrne HM,Chaplin MA

    更新日期:1996-07-15 00:00:00

  • Coherent potential approximation approach to electronic structure of DNA.

    abstract::The electronic structure of DNA is theoretically investigated by use of the coherent potential approximation. Even when the sequence of the four kinds of bases is nonperiodic, guanine block forms the persistent highest valence band edge, and adenine block forms the persistent lowest conduction band edge state. Accordi...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/0025-5564(94)00118-5

    authors: Takeda K

    更新日期:1995-12-01 00:00:00

  • Stochastic optimal therapy for enhanced immune response.

    abstract::Therapeutic enhancement of humoral immune response to microbial attack is addressed as the stochastic optimal control of a dynamic system. Without therapy, the modeled immune response depends upon the initial concentration of pathogens in a simulated attack. Immune response can be augmented by agents that kill the pat...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2004.06.004

    authors: Stengel RF,Ghigliazza R

    更新日期:2004-10-01 00:00:00

  • Scaffold-mediated nucleation of protein signaling complexes: elementary principles.

    abstract::Proteins with multiple binding sites play important roles in cell signaling systems by nucleating protein complexes in which, for example, enzymes and substrates are co-localized. Proteins that specialize in this function are called by a variety names, including adapter, linker and scaffold. Scaffold-mediated nucleati...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2011.06.003

    authors: Yang J,Hlavacek WS

    更新日期:2011-08-01 00:00:00

  • A geometrical model for diffusion of hydrophilic compounds in human stratum corneum.

    abstract::A three-dimensional diffusion model with either hexagonal or cylindrical symmetry has been constructed to simulate desorption profiles of hydrophilic chemicals from the topmost layer of human skin (the stratum corneum) as measured in ex vivo studies. The tissue is pierced by skin appendages - sweat glands and hair fol...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2018.03.010

    authors: Yu F,Kasting GB

    更新日期:2018-06-01 00:00:00

  • Quantification of the effect of control strategies on classical swine fever epidemics.

    abstract::Emergency vaccination during an epidemic of classical swine fever virus (CSFV) has become a serious option because of the ethical problems of strategies with massive culling and the availability of a marker vaccine that reduces virus transmission. Here we present a model of between-herd CSFV transmission, which quanti...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2003.08.005

    authors: Klinkenberg D,Everts-van der Wind A,Graat EA,de Jong MC

    更新日期:2003-12-01 00:00:00

  • Persistence of an infectious disease in a subdivided population.

    abstract::The transmission dynamics of a communicable disease in a subdivided population where the spread among groups follows the proportionate mixing model while the within-group transmission can correspond to preferred mixing, proportionate mixing among subgroups, or mixing between social and nonsocial subgroups, is analyzed...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/0025-5564(89)90061-8

    authors: Andreasen V,Christiansen FB

    更新日期:1989-10-01 00:00:00

  • The optimal strategy for brood-parasitism: how many eggs should be laid in the host's nest?

    abstract::We consider the optimal strategy for intra-specific brood-parasitism, especially with respect to the number of eggs laid by the parasitic individual in the nest of non-parasitic individual, in particular, a host that does not reject the parasite's eggs. With a fundamental mathematical model, assuming that the survival...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/s0025-5564(99)00037-1

    authors: Maruyama J,Seno H

    更新日期:1999-10-01 00:00:00

  • Prediction of N-linked glycan branching patterns using artificial neural networks.

    abstract::A model was developed for novel prediction of N-linked glycan branching pattern classification for CHO-derived N-linked glycoproteins. The model consists of 30 independent recurrent neural networks and uses predicted quantities of secondary structure elements and residue solvent accessibility as an input vector. The m...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2007.10.005

    authors: Senger RS,Karim MN

    更新日期:2008-01-01 00:00:00

  • Biological growth on a surface.

    abstract::A new biological growth model is introduced. After random selection of possible growth sites, cells are added in an allowable random direction. Unlike the Eden model, the current model is grid independent and can be adapted to any curved surface. Growths of colonies of as many as 10(5) cells are simulated on planar, c...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/s0025-5564(97)00012-6

    authors: Wang CY,Bassingthwaighte JB

    更新日期:1997-06-01 00:00:00

  • Genetic oscillation deduced from Hopf bifurcation in a genetic regulatory network with delays.

    abstract::To understand how a gene regulatory network functioning as an oscillator is built, a genetic regulatory network with two transcriptional delays is investigated. We show by mathematical analysis and simulation that autorepression of mRNA and protein can provide a mechanism for the intracellular oscillator. Based on the...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2008.05.004

    authors: Xiao M,Cao J

    更新日期:2008-09-01 00:00:00

  • Resistance of a food chain to invasion by a top predator.

    abstract::We study the invasion of a top predator into a food chain in a chemostat. For each trophic level, a bioenergetic model is used in which maintenance and energy reserves are taken into account. Bifurcation analysis is performed on the set of nonlinear ordinary differential equations which describe the dynamic behaviour ...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/s0025-5564(98)10083-4

    authors: Kooi BW,Boer MP,Kooijman SA

    更新日期:1999-03-15 00:00:00

  • Yule-generated trees constrained by node imbalance.

    abstract::The Yule process generates a class of binary trees which is fundamental to population genetic models and other applications in evolutionary biology. In this paper, we introduce a family of sub-classes of ranked trees, called Ω-trees, which are characterized by imbalance of internal nodes. The degree of imbalance is de...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2013.08.008

    authors: Disanto F,Schlizio A,Wiehe T

    更新日期:2013-11-01 00:00:00

  • Mathematics of protein pathological misfolding.

    abstract::"Protein folding is defined as a process by which a polypeptide chain performs a search in conformational space with the objective of achieving the so-called native conformation to global free-energy minimum under a given set of physiochemical conditions of the medium." Misfolding then, is the process by which this ob...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章,评审

    doi:10.1016/j.mbs.2006.08.008

    authors: Armah EO

    更新日期:2007-07-01 00:00:00

  • A one-dimensional map to study multi-seasonal coffee infestation by the coffee berry borer.

    abstract::The coffee berry borer (CBB, Hypothenemus hampei) is the most serious insect pest of coffee worldwide; understanding the dynamics of its reproduction is essential for pest management. The female CBB penetrates the coffee berry, eats the seed, and reproduces inside it. A mathematical model of the infestation progress o...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2020.108530

    authors: Marcano M,Bose A,Bayman P

    更新日期:2021-01-21 00:00:00

  • Deterministic epidemic models with explicit household structure.

    abstract::For a wide range of airborne infectious diseases, transmission within the family or household is a key mechanism for the spread and persistence of infection. In general, household-based transmission is relatively strong but only involves a limited number of individuals in contact with each infectious person. In contra...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2008.01.011

    authors: House T,Keeling MJ

    更新日期:2008-05-01 00:00:00

  • Dependence of mating rate on variance of eclosion time of cicadas (cicadidae).

    abstract::In many cicadas, a phenomenon is observed in which the peak of emergence of males precedes that of females (protandry). Generally, it is known that the ecology of emergence of insects is closely related to mating, and protandry is said to be the strategy of males to eclose early and to attempt mating with virgin femal...

    journal_title:Mathematical biosciences

    pub_type: 杂志文章

    doi:10.1016/j.mbs.2018.08.006

    authors: Saisho Y

    更新日期:2018-11-01 00:00:00