Monte Carlo simulation in phylogenies: An application to test the constancy of evolutionary rates

Adell, J C; Dopazo, Joaquı́n

doi:10.1007/bf00176093

Cited by 21 publications

(12 citation statements)

References 35 publications

(31 reference statements)

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“…Relative rate tests.-Evaluation of rate homogeneity was performed using two different approaches: (1) relative rate tests of sequence evolution according to the Tajima (1993) 1D method, with sequential Bonferroni correction for multiple testing (Rice, 1989); and (2) simulation of a null distribution specific to the sampled gene and taxa (e.g., Adell and Dopazo, 1994). We employed the latter to obtain a sampling distribution for the null hypothesis of a molecular clock.…”

Section: Cyt B Sequences From Notemigonus Crysoleucas Andmentioning

confidence: 99%

Molecular Phylogenetics and Evolution of the Cytochrome b Gene in the Cyprinid Genus Lythrurus (Actinopterygii: Cypriniformes)

Schmidt¹,

Bielawski²,

Gold³

1998

Copeia

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Section: Cyt B Sequences From Notemigonus Crysoleucas Andmentioning

confidence: 99%

Molecular Phylogenetics and Evolution of the Cytochrome b Gene in the Cyprinid Genus Lythrurus (Actinopterygii: Cypriniformes)

Schmidt¹,

Bielawski²,

Gold³

1998

Copeia

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“…This simplicity is in contrast to potential Monte Carlo tests (e.g., Adell and Dopazo, 1994) where this information must be supplied or assumed. While the permutation tests described here also make use of phylogenetic information, they do not require new trees to be estimated for different subsequences.…”

Section: Resultsmentioning

confidence: 92%

Searching for Substitution Rate Heterogeneity

Hartmann

Golding

1998

Molecular Phylogenetics and Evolution

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“…Simulations of evolutionary process are widely used to test phylogenetic methods such as evolutionary distance estimation and tree reconstruction (26,27). Our design procedure can be viewed as a simulation of evolutionary process in which stability and function are taken into account in the selective fixation of substitutions.…”

Section: Design and Functional Residue Identificationmentioning

confidence: 99%

Using protein design for homology detection and active site searches

Pei

Dokholyan

Shakhnovich

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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We describe a method of designing artificial sequences that resemble naturally occurring sequences in terms of their compatibility with a template structure and its functional constraints. The design procedure is a Monte Carlo simulation of amino acid substitution process. The selective fixation of substitutions is dictated by a simple scoring function derived from the template structure and a multiple alignment of its homologs. Designed sequences represent an enlargement of sequence space around native sequences. We show that the use of designed sequences improves the performance of profile-based homology detection. The difference in position-specific conservation between designed sequences and native sequences is helpful for prediction of functionally important residues. Our sequence selection criteria in evolutionary simulations introduce amino acid substitution rate variation among sites in a natural way, providing a better model to test phylogenetic methods. C omputational protein design aims to identify sequences compatible with a desired structure or fold (1-4). Most design methods involve detailed energy functions with explicit modeling of protein structure at the atomic level and apply effective search algorithms (5, 6). They facilitate understanding of the physical and chemical principles governing protein structure and folding (4). Protein design can also be used to probe the sequence space (7), which has been applied in fold recognition (8). This idea can be extended to profile-based similarity searches, which derive a scoring function based on a multiple sequence alignment. Designed sequences resembling naturally occurring sequences could potentially be used to improve sequence profile, leading to more powerful homology detection. Sequence design can also be used in studying protein function and evolution (9, 10), as it is often related to evolutionary simulations. It is generally assumed that amino acid changes follow a stochastic process over long periods of time, and the fixation of substitutions is under evolutionary pressure to preserve protein activity. Evolutionary simulations can be made more realistic if structural and functional constraints are taken into account in the substitution process.Knowledge-based approaches have been widely used to derive interaction potentials by statistical analysis of known protein structures (11,12). Such potentials are used in various sequence design methods as stability constraints. Functional information about a protein family is embedded in naturally occurring homologs as positional amino acid conservation. Sequence profile, such as the position-specific scoring matrix generated by PSI-BLAST (13), contains the positional conservation information. We attempt to introduce structural and functional constraints in sequence design by considering both pairwise interaction potentials and sequence conservation information.Recently, a simulation-based design method (Z-score model) was used to study the protein evolutionary process (10). Structurally similar sequen...

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Monte Carlo simulation in phylogenies: An application to test the constancy of evolutionary rates

Cited by 21 publications

References 35 publications

Molecular Phylogenetics and Evolution of the Cytochrome b Gene in the Cyprinid Genus Lythrurus (Actinopterygii: Cypriniformes)

Molecular Phylogenetics and Evolution of the Cytochrome b Gene in the Cyprinid Genus Lythrurus (Actinopterygii: Cypriniformes)

Searching for Substitution Rate Heterogeneity

Using protein design for homology detection and active site searches

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