Search Results - subject:"molecular evolution"

In defence of model-based inference in phylogeography

Corander, Jukka; Panchal, Mahesh; Gaggiotti, Oscar; … - Université Paris-Dauphine (Paris IX) - 2010

Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested...

Persistent link: https://www.econbiz.de/10010707765

Genetic code evolution as an initial driving force for molecular evolution

Li, Dirson Jian; Zhang, Shengli - In: Physica A: Statistical Mechanics and its Applications 388 (2009) 18, pp. 3809-3825

There is an intrinsic relationship between the molecular evolution in primordial period and genomic or proteomic … level. In the absence of evidence, numerous problems in molecular evolution had to fall into a twilight zone of speculation … frequencies resulted from the genetic code evolution, which underlies the molecular evolution. The theoretical results agree with …

Persistent link: https://www.econbiz.de/10010589396

Statistical Inference in Evolutionary Models of DNA Sequences via the EM Algorithm

Hobolth, Asger; Jensen, Jens - In: Statistical Applications in Genetics and Molecular Biology 4 (2007) 1, pp. 18-18

We describe statistical inference in continuous time Markov processes of DNA sequences related by a phylogenetic tree. The maximum likelihood estimator can be found by the expectation maximization (EM) algorithm and an expression for the information matrix is also derived. We provide explicit...

Persistent link: https://www.econbiz.de/10005585061

COMPACTNESS AND CYCLES IN SIGNAL TRANSDUCTION AND TRANSCRIPTIONAL REGULATION NETWORKS: A SIGNATURE OF NATURAL SELECTION?

WAGNER, ANDREAS; WRIGHT, JEREMIAH - In: Advances in Complex Systems (ACS) 07 (2004) 03, pp. 419-432

We ask whether natural selection has shaped three biologically important features of 15 signal transduction networks and two genome-scale transcriptional regulation networks. These features are regulatory cycles, the lengths of the longest pathways through a network — a measure of network...

Persistent link: https://www.econbiz.de/10004977697

Mutational Robustness and Asymmetric Functional Specialization of Duplicate Genes

Wagner, Andreas - Santa Fe Institute - 2002

Most duplicate genes are eliminated from a genome shortly after duplication, but those that remain are an important source of biochemical diversity. Much of their diversification arises via functional ÒspecializationÓ, loss of some functions of the duplicates remaining in the genome. I here...

Persistent link: https://www.econbiz.de/10005790970

Dynamic fitness landscapes: expansions for small mutation rates

Wilke, Claus O.; Ronnewinkel, Christopher - In: Physica A: Statistical Mechanics and its Applications 290 (2001) 3, pp. 475-490

We study the evolution of asexual microorganisms with small mutation rate in fluctuating environments, and develop techniques that allow us to expand the formal solution of the evolution equations to first order in the mutation rate. Our method can be applied to both discrete time and continuous...

Persistent link: https://www.econbiz.de/10010872872

Nature and Evolution of Early Replicons

Schuster, Peter; Stadler, Peter F. - Santa Fe Institute - 1998

RNA and protein molecules were found to be both templates for replication and specific catalysts for biochemical reactions. RNA molecules, although very difficult to obtain via plausible synthetic pathways under prebiotic conditions, are the only candidates for early replicons. Only they are...

Persistent link: https://www.econbiz.de/10005790890

Fitness Landscapes Arising from the Sequence-Structure Maps of Biopolymers

Stadler, Peter F. - Santa Fe Institute - 1997

Fitness landscapes are an important concept in molecular evolution since evolutionary adaptation as well as {\it in …

Persistent link: https://www.econbiz.de/10005623634

Sequence Redundancy in Biopolymers: A Study on RNA and Protein Structures

Schuster, Peter; Stadler, Peter F. - Santa Fe Institute - 1997

Mapping sequences onto biopolymer structures is characterized by redundancy since the numbers of sequences exceed the numbers of structures. The degree of Redundancy depends on the notion of structure. Two classes of biopolymers, RNA molecules and proteins are considered in detail. A general...

Persistent link: https://www.econbiz.de/10005739913

Stochastic Modeling and Optimization of Phage Display

Levitan, Bennett - Santa Fe Institute - 1997

Phage display, SELEX and other methods of combinatorial chemistry have become very popular means of finding ligands with high affinities to given targets. Despite their success, they suffer from numerous sources of error and bias, such as very low initial concentrations of species, non-specific...

Persistent link: https://www.econbiz.de/10005790639