Literature DB >> 25167038

Neutral evolution of duplicated DNA: an evolutionary stick-breaking process causes scale-invariant behavior.

Florian Massip1, Peter F Arndt1.   

Abstract

Recently, an enrichment of identical matching sequences has been found in many eukaryotic genomes. Their length distribution exhibits a power law tail raising the question of what evolutionary mechanism or functional constraints would be able to shape this distribution. Here we introduce a simple and evolutionarily neutral model, which involves only point mutations and segmental duplications, and produces the same statistical features as observed for genomic data. Further, we extend a mathematical model for random stick breaking to analytically show that the exponent of the power law tail is -3 and universal as it does not depend on the microscopic details of the model.

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Year:  2013        PMID: 25167038     DOI: 10.1103/PhysRevLett.110.148101

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  9 in total

1.  Comparing the Statistical Fate of Paralogous and Orthologous Sequences.

Authors:  Florian Massip; Michael Sheinman; Sophie Schbath; Peter F Arndt
Journal:  Genetics       Date:  2016-07-29       Impact factor: 4.562

2.  Diminishing return for increased Mappability with longer sequencing reads: implications of the k-mer distributions in the human genome.

Authors:  Wentian Li; Jan Freudenberg; Pedro Miramontes
Journal:  BMC Bioinformatics       Date:  2014-01-03       Impact factor: 3.169

Review 3.  Mappability and read length.

Authors:  Wentian Li; Jan Freudenberg
Journal:  Front Genet       Date:  2014-11-10       Impact factor: 4.599

4.  How evolution of genomes is reflected in exact DNA sequence match statistics.

Authors:  Florian Massip; Michael Sheinman; Sophie Schbath; Peter F Arndt
Journal:  Mol Biol Evol       Date:  2014-11-13       Impact factor: 16.240

5.  Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences.

Authors:  Michael Sheinman; Anna Ramisch; Florian Massip; Peter F Arndt
Journal:  Sci Rep       Date:  2016-08-04       Impact factor: 4.379

6.  Size distribution of function-based human gene sets and the split-merge model.

Authors:  Wentian Li; Oscar Fontanelli; Pedro Miramontes
Journal:  R Soc Open Sci       Date:  2016-08-03       Impact factor: 2.963

7.  Primary orthologs from local sequence context.

Authors:  Kun Gao; Jonathan Miller
Journal:  BMC Bioinformatics       Date:  2020-02-06       Impact factor: 3.169

8.  Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain.

Authors:  Michael Sheinman; Ksenia Arkhipova; Rutger Hermsen; Florian Massip; Peter F Arndt; Bas E Dutilh
Journal:  Elife       Date:  2021-06-14       Impact factor: 8.140

9.  A Model-Driven Quantitative Analysis of Retrotransposon Distributions in the Human Genome.

Authors:  Andrea Riba; Maria Rita Fumagalli; Michele Caselle; Matteo Osella
Journal:  Genome Biol Evol       Date:  2020-11-03       Impact factor: 3.416

  9 in total

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